From 4459b6d5117d536721f540dd35ad622730d698b3 Mon Sep 17 00:00:00 2001 From: Deepak Unni Date: Mon, 8 Nov 2021 22:07:26 +0000 Subject: [PATCH] Regenerate artifacts from biolink-model.yaml --- biolink-model.owl.ttl | 782 +++++++++++++++++++++--------------------- biolink-model.ttl | 498 +++++++++++++-------------- biolink/model.py | 6 +- context.jsonld | 8 +- contextn.jsonld | 8 +- 5 files changed, 651 insertions(+), 651 deletions(-) diff --git a/biolink-model.owl.ttl b/biolink-model.owl.ttl index f64a3ef706..ff2b923d8e 100644 --- a/biolink-model.owl.ttl +++ b/biolink-model.owl.ttl @@ -77,11 +77,11 @@ dcat:downloadURL a owl:ObjectProperty . dct:license "https://creativecommons.org/publicdomain/zero/1.0/" ; pav:version "2.2.9" ; skos:definition "Entity and association taxonomy and datamodel for life-sciences data" ; - linkml:generation_date "2021-11-08T21:40:02" ; + linkml:generation_date "2021-11-08T22:04:50" ; linkml:metamodel_version "1.7.0" ; linkml:source_file "biolink-model.yaml" ; - linkml:source_file_date "2021-11-08T21:37:13" ; - linkml:source_file_size 325053 . + linkml:source_file_date "2021-11-08T22:02:12" ; + linkml:source_file_size 325059 . biolink:Activity a owl:Class ; rdfs:label "activity" ; @@ -102,16 +102,16 @@ biolink:Activity a owl:Class ; biolink:AnatomicalEntityToAnatomicalEntityOntogenicAssociation a owl:Class ; rdfs:label "anatomical entity to anatomical entity ontogenic association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:onClass biolink:AnatomicalEntity ; - owl:onProperty rdf:object ; + owl:onClass biolink:PredicateType ; + owl:onProperty rdf:predicate ; owl:qualifiedCardinality 1 ], [ a owl:Restriction ; owl:onClass biolink:AnatomicalEntity ; owl:onProperty rdf:subject ; owl:qualifiedCardinality 1 ], [ a owl:Restriction ; - owl:onClass biolink:PredicateType ; - owl:onProperty rdf:predicate ; + owl:onClass biolink:AnatomicalEntity ; + owl:onProperty rdf:object ; owl:qualifiedCardinality 1 ], 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." . @@ -136,13 +136,13 @@ biolink:AnatomicalEntityToAnatomicalEntityPartOfAssociation a owl:Class ; biolink:Article a owl:Class ; rdfs:label "article" ; rdfs:subClassOf [ a owl:Restriction ; - owl:onClass linkml:Uriorcurie ; - owl:onProperty biolink:published_in ; - owl:qualifiedCardinality 1 ], - [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass linkml:String ; owl:onProperty biolink:iso_abbreviation ], + [ a owl:Restriction ; + owl:onClass linkml:Uriorcurie ; + owl:onProperty biolink:published_in ; + owl:qualifiedCardinality 1 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass linkml:String ; @@ -156,14 +156,6 @@ biolink:Article a owl:Class ; biolink:BehaviorToBehavioralFeatureAssociation a owl:Class ; rdfs:label "behavior to behavioral feature association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:SeverityValue ; - owl:onProperty biolink:severity_qualifier ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:BiologicalSex ; - owl:onProperty biolink:sex_qualifier ], - [ a owl:Restriction ; owl:onClass biolink:Behavior ; owl:onProperty rdf:subject ; owl:qualifiedCardinality 1 ], @@ -171,10 +163,18 @@ biolink:BehaviorToBehavioralFeatureAssociation a owl:Class ; owl:maxQualifiedCardinality 1 ; owl:onClass biolink:Onset ; owl:onProperty biolink:onset_qualifier ], + [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass biolink:BiologicalSex ; + owl:onProperty biolink:sex_qualifier ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass biolink:FrequencyValue ; owl:onProperty biolink:frequency_qualifier ], + [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass biolink:SeverityValue ; + owl:onProperty biolink:severity_qualifier ], [ a owl:Restriction ; owl:onClass biolink:BehavioralFeature ; owl:onProperty rdf:object ; @@ -212,11 +212,11 @@ biolink:Book a owl:Class ; rdfs:label "book" ; rdfs:subClassOf [ a owl:Restriction ; owl:onClass linkml:String ; - owl:onProperty rdf:type ; + owl:onProperty biolink:id ; owl:qualifiedCardinality 1 ], [ a owl:Restriction ; owl:onClass linkml:String ; - owl:onProperty biolink:id ; + owl:onProperty rdf:type ; owl:qualifiedCardinality 1 ], biolink:Publication ; skos:definition "This class may rarely be instantiated except if use cases of a given knowledge graph support its utility." . @@ -225,20 +225,20 @@ biolink:CaseToPhenotypicFeatureAssociation a owl:Class ; rdfs:label "case to phenotypic feature association" ; rdfs:subClassOf [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:SeverityValue ; - owl:onProperty biolink:severity_qualifier ], + owl:onClass biolink:FrequencyValue ; + owl:onProperty biolink:frequency_qualifier ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass biolink:Onset ; owl:onProperty biolink:onset_qualifier ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:BiologicalSex ; - owl:onProperty biolink:sex_qualifier ], + owl:onClass biolink:SeverityValue ; + owl:onProperty biolink:severity_qualifier ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:FrequencyValue ; - owl:onProperty biolink:frequency_qualifier ], + owl:onClass biolink:BiologicalSex ; + owl:onProperty biolink:sex_qualifier ], biolink:Association, biolink:CaseToEntityAssociationMixin, biolink:EntityToPhenotypicFeatureAssociationMixin ; @@ -256,21 +256,21 @@ 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:maxQualifiedCardinality 1 ; + owl:onClass biolink:Onset ; + owl:onProperty biolink:onset_qualifier ], + [ a owl:Restriction ; owl:onClass biolink:CellLine ; owl:onProperty rdf:subject ; owl:qualifiedCardinality 1 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:Onset ; - owl:onProperty biolink:onset_qualifier ], + owl:onClass biolink:SeverityValue ; + owl:onProperty biolink:severity_qualifier ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass biolink:FrequencyValue ; owl:onProperty biolink:frequency_qualifier ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:SeverityValue ; - owl:onProperty biolink:severity_qualifier ], biolink:CellLineToDiseaseOrPhenotypicFeatureAssociation, biolink:EntityToDiseaseAssociationMixin, biolink:ModelToDiseaseAssociationMixin . @@ -278,19 +278,19 @@ biolink:CellLineAsAModelOfDiseaseAssociation a owl:Class ; biolink:ChemicalToChemicalDerivationAssociation a owl:Class ; rdfs:label "chemical to chemical derivation association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:onClass biolink:ChemicalEntity ; - owl:onProperty rdf:object ; - owl:qualifiedCardinality 1 ], - [ a owl:Restriction ; owl:allValuesFrom biolink:MacromolecularMachineMixin ; owl:onProperty biolink:catalyst_qualifier ], + [ a owl:Restriction ; + owl:onClass biolink:PredicateType ; + owl:onProperty rdf:predicate ; + owl:qualifiedCardinality 1 ], [ a owl:Restriction ; owl:onClass biolink:ChemicalEntity ; owl:onProperty rdf:subject ; owl:qualifiedCardinality 1 ], [ a owl:Restriction ; - owl:onClass biolink:PredicateType ; - owl:onProperty rdf:predicate ; + owl:onClass biolink:ChemicalEntity ; + owl:onProperty rdf:object ; owl:qualifiedCardinality 1 ], biolink:ChemicalToChemicalAssociation ; skos:definition """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: @@ -376,20 +376,20 @@ biolink:ComplexMolecularMixture a owl:Class ; biolink:ContributorAssociation a owl:Class ; rdfs:label "contributor association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom biolink:OntologyClass ; - owl:onProperty biolink:qualifiers ], - [ a owl:Restriction ; owl:onClass biolink:PredicateType ; owl:onProperty rdf:predicate ; owl:qualifiedCardinality 1 ], [ a owl:Restriction ; - owl:onClass biolink:InformationContentEntity ; - owl:onProperty rdf:subject ; - owl:qualifiedCardinality 1 ], + owl:allValuesFrom biolink:OntologyClass ; + owl:onProperty biolink:qualifiers ], [ a owl:Restriction ; owl:onClass biolink:Agent ; owl:onProperty rdf:object ; owl:qualifiedCardinality 1 ], + [ a owl:Restriction ; + owl:onClass biolink:InformationContentEntity ; + owl:onProperty rdf:subject ; + owl:qualifiedCardinality 1 ], biolink:Association ; skos:definition "Any association between an entity (such as a publication) and various agents that contribute to its realisation" . @@ -429,8 +429,8 @@ biolink:DiseaseToPhenotypicFeatureAssociation a owl:Class ; rdfs:label "disease to phenotypic feature association" ; rdfs:subClassOf [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:Onset ; - owl:onProperty biolink:onset_qualifier ], + owl:onClass biolink:FrequencyValue ; + owl:onProperty biolink:frequency_qualifier ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass biolink:BiologicalSex ; @@ -441,8 +441,8 @@ biolink:DiseaseToPhenotypicFeatureAssociation a owl:Class ; owl:onProperty biolink:severity_qualifier ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:FrequencyValue ; - owl:onProperty biolink:frequency_qualifier ], + owl:onClass biolink:Onset ; + owl:onProperty biolink:onset_qualifier ], biolink:Association, biolink:DiseaseToEntityAssociationMixin, biolink:EntityToPhenotypicFeatureAssociationMixin ; @@ -516,13 +516,13 @@ biolink:Event a owl:Class ; biolink:ExonToTranscriptRelationship a owl:Class ; rdfs:label "exon to transcript relationship" ; rdfs:subClassOf [ a owl:Restriction ; - owl:onClass biolink:Transcript ; - owl:onProperty rdf:object ; - owl:qualifiedCardinality 1 ], - [ a owl:Restriction ; owl:onClass biolink:Exon ; owl:onProperty rdf:subject ; owl:qualifiedCardinality 1 ], + [ a owl:Restriction ; + owl:onClass biolink:Transcript ; + owl:onProperty rdf:object ; + owl:qualifiedCardinality 1 ], biolink:SequenceFeatureRelationship ; skos:definition "A transcript is formed from multiple exons" . @@ -544,6 +544,14 @@ biolink:ExposureEventToOutcomeAssociation a owl:Class ; biolink:ExposureEventToPhenotypicFeatureAssociation a owl:Class ; rdfs:label "exposure event to phenotypic feature association" ; rdfs:subClassOf [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass biolink:Onset ; + owl:onProperty biolink:onset_qualifier ], + [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass biolink:SeverityValue ; + owl:onProperty biolink:severity_qualifier ], + [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass biolink:FrequencyValue ; owl:onProperty biolink:frequency_qualifier ], @@ -551,18 +559,10 @@ biolink:ExposureEventToPhenotypicFeatureAssociation a owl:Class ; owl:maxQualifiedCardinality 1 ; owl:onClass biolink:BiologicalSex ; owl:onProperty biolink:sex_qualifier ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:SeverityValue ; - owl:onProperty biolink:severity_qualifier ], [ a owl:Restriction ; owl:onClass biolink:ExposureEvent ; owl:onProperty rdf:subject ; owl:qualifiedCardinality 1 ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:Onset ; - owl:onProperty biolink:onset_qualifier ], biolink:Association, biolink:EntityToPhenotypicFeatureAssociationMixin ; skos:definition "Any association between an environment and a phenotypic feature, where being in the environment influences the phenotype." . @@ -608,25 +608,25 @@ biolink:GeneFamily a owl:Class ; biolink:GeneHasVariantThatContributesToDiseaseAssociation a owl:Class ; rdfs:label "gene has variant that contributes to disease association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:SequenceVariant ; - owl:onProperty biolink:sequence_variant_qualifier ], - [ a owl:Restriction ; owl:onClass biolink:GeneOrGeneProduct ; owl:onProperty rdf:subject ; owl:qualifiedCardinality 1 ], + [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass biolink:SequenceVariant ; + owl:onProperty biolink:sequence_variant_qualifier ], biolink:GeneToDiseaseAssociation . biolink:GeneRegulatoryRelationship a owl:Class ; rdfs:label "gene regulatory relationship" ; rdfs:subClassOf [ a owl:Restriction ; - owl:onClass biolink:GeneOrGeneProduct ; - owl:onProperty rdf:object ; - owl:qualifiedCardinality 1 ], - [ a owl:Restriction ; owl:onClass biolink:PredicateType ; owl:onProperty rdf:predicate ; owl:qualifiedCardinality 1 ], + [ a owl:Restriction ; + owl:onClass biolink:GeneOrGeneProduct ; + owl:onProperty rdf:object ; + owl:qualifiedCardinality 1 ], [ a owl:Restriction ; owl:onClass biolink:GeneOrGeneProduct ; owl:onProperty rdf:subject ; @@ -645,6 +645,10 @@ biolink:GeneToExpressionSiteAssociation a owl:Class ; owl:onClass biolink:PredicateType ; owl:onProperty rdf:predicate ; owl:qualifiedCardinality 1 ], + [ a owl:Restriction ; + owl:onClass biolink:GeneOrGeneProduct ; + owl:onProperty rdf:subject ; + owl:qualifiedCardinality 1 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass biolink:OntologyClass ; @@ -653,10 +657,6 @@ biolink:GeneToExpressionSiteAssociation a owl:Class ; owl:onClass biolink:AnatomicalEntity ; owl:onProperty rdf:object ; owl:qualifiedCardinality 1 ], - [ a owl:Restriction ; - owl:onClass biolink:GeneOrGeneProduct ; - owl:onProperty rdf:subject ; - owl:qualifiedCardinality 1 ], biolink:Association ; skos:definition "An association between a gene and an expression site, possibly qualified by stage/timing info." ; skos:editorialNote "TBD: introduce subclasses for distinction between wild-type and experimental conditions?" . @@ -664,21 +664,21 @@ biolink:GeneToExpressionSiteAssociation a owl:Class ; biolink:GeneToGeneCoexpressionAssociation a owl:Class ; rdfs:label "gene to gene coexpression association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:onClass biolink:PredicateType ; - owl:onProperty rdf:predicate ; - owl:qualifiedCardinality 1 ], - [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass biolink:DiseaseOrPhenotypicFeature ; owl:onProperty biolink:phenotypic_state ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:AnatomicalEntity ; - owl:onProperty biolink:expression_site ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass biolink:LifeStage ; owl:onProperty biolink:stage_qualifier ], + [ a owl:Restriction ; + owl:onClass biolink:PredicateType ; + owl:onProperty rdf:predicate ; + owl:qualifiedCardinality 1 ], + [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass biolink:AnatomicalEntity ; + owl:onProperty biolink:expression_site ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass biolink:OntologyClass ; @@ -699,13 +699,13 @@ biolink:GeneToGeneHomologyAssociation a owl:Class ; biolink:GeneToGeneProductRelationship a owl:Class ; rdfs:label "gene to gene product relationship" ; rdfs:subClassOf [ a owl:Restriction ; - owl:onClass biolink:GeneProductMixin ; - owl:onProperty rdf:object ; - owl:qualifiedCardinality 1 ], - [ a owl:Restriction ; owl:onClass biolink:PredicateType ; owl:onProperty rdf:predicate ; owl:qualifiedCardinality 1 ], + [ a owl:Restriction ; + owl:onClass biolink:GeneProductMixin ; + owl:onProperty rdf:object ; + owl:qualifiedCardinality 1 ], [ a owl:Restriction ; owl:onClass biolink:Gene ; owl:onProperty rdf:subject ; @@ -730,14 +730,6 @@ biolink:GeneToGoTermAssociation a owl:Class ; biolink:GeneToPhenotypicFeatureAssociation a owl:Class ; rdfs:label "gene to phenotypic feature association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:SeverityValue ; - owl:onProperty biolink:severity_qualifier ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:FrequencyValue ; - owl:onProperty biolink:frequency_qualifier ], - [ a owl:Restriction ; owl:onClass biolink:GeneOrGeneProduct ; owl:onProperty rdf:subject ; owl:qualifiedCardinality 1 ], @@ -749,6 +741,14 @@ biolink:GeneToPhenotypicFeatureAssociation a owl:Class ; owl:maxQualifiedCardinality 1 ; owl:onClass biolink:Onset ; owl:onProperty biolink:onset_qualifier ], + [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass biolink:FrequencyValue ; + owl:onProperty biolink:frequency_qualifier ], + [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass biolink:SeverityValue ; + owl:onProperty biolink:severity_qualifier ], biolink:Association, biolink:EntityToPhenotypicFeatureAssociationMixin, biolink:GeneToEntityAssociationMixin ; @@ -775,19 +775,19 @@ biolink:Genome a owl:Class ; biolink:GenomicBackgroundExposure a owl:Class ; rdfs:label "genomic background exposure" ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom biolink:OrganismTaxon ; - owl:onProperty biolink:in_taxon ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:BiologicalSequence ; - owl:onProperty biolink:has_biological_sequence ], - [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass biolink:TimeType ; owl:onProperty biolink:timepoint ], [ a owl:Restriction ; owl:allValuesFrom biolink:Gene ; owl:onProperty biolink:has_gene_or_gene_product ], + [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass biolink:BiologicalSequence ; + owl:onProperty biolink:has_biological_sequence ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:OrganismTaxon ; + owl:onProperty biolink:in_taxon ], biolink:ExposureEvent, biolink:GeneGroupingMixin, biolink:GenomicEntity, @@ -825,10 +825,6 @@ biolink:GenotypeToGeneAssociation a owl:Class ; biolink:GenotypeToGenotypePartAssociation a owl:Class ; rdfs:label "genotype to genotype part association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:onClass biolink:Genotype ; - owl:onProperty rdf:object ; - owl:qualifiedCardinality 1 ], - [ a owl:Restriction ; owl:onClass biolink:Genotype ; owl:onProperty rdf:subject ; owl:qualifiedCardinality 1 ], @@ -836,6 +832,10 @@ biolink:GenotypeToGenotypePartAssociation a owl:Class ; owl:onClass biolink:PredicateType ; owl:onProperty rdf:predicate ; owl:qualifiedCardinality 1 ], + [ a owl:Restriction ; + owl:onClass biolink:Genotype ; + owl:onProperty rdf:object ; + owl:qualifiedCardinality 1 ], biolink:Association ; skos:definition "Any association between one genotype and a genotypic entity that is a sub-component of it" . @@ -843,28 +843,28 @@ biolink:GenotypeToPhenotypicFeatureAssociation a owl:Class ; rdfs:label "genotype to phenotypic feature association" ; rdfs:subClassOf [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:SeverityValue ; - owl:onProperty biolink:severity_qualifier ], + owl:onClass biolink:FrequencyValue ; + owl:onProperty biolink:frequency_qualifier ], [ a owl:Restriction ; owl:onClass biolink:PredicateType ; owl:onProperty rdf:predicate ; owl:qualifiedCardinality 1 ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:BiologicalSex ; - owl:onProperty biolink:sex_qualifier ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:FrequencyValue ; - owl:onProperty biolink:frequency_qualifier ], [ a owl:Restriction ; owl:onClass biolink:Genotype ; owl:onProperty rdf:subject ; owl:qualifiedCardinality 1 ], + [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass biolink:SeverityValue ; + owl:onProperty biolink:severity_qualifier ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass biolink:Onset ; owl:onProperty biolink:onset_qualifier ], + [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass biolink:BiologicalSex ; + owl:onProperty biolink:sex_qualifier ], biolink:Association, biolink:EntityToPhenotypicFeatureAssociationMixin, biolink:GenotypeToEntityAssociationMixin ; @@ -873,6 +873,10 @@ biolink:GenotypeToPhenotypicFeatureAssociation a owl:Class ; biolink:GenotypeToVariantAssociation a owl:Class ; rdfs:label "genotype to variant association" ; rdfs:subClassOf [ a owl:Restriction ; + owl:onClass biolink:PredicateType ; + owl:onProperty rdf:predicate ; + owl:qualifiedCardinality 1 ], + [ a owl:Restriction ; owl:onClass biolink:SequenceVariant ; owl:onProperty rdf:object ; owl:qualifiedCardinality 1 ], @@ -880,10 +884,6 @@ biolink:GenotypeToVariantAssociation a owl:Class ; owl:onClass biolink:Genotype ; owl:onProperty rdf:subject ; owl:qualifiedCardinality 1 ], - [ a owl:Restriction ; - owl:onClass biolink:PredicateType ; - owl:onProperty rdf:predicate ; - owl:qualifiedCardinality 1 ], biolink:Association ; skos:definition "Any association between a genotype and a sequence variant." . @@ -922,12 +922,12 @@ biolink:GrossAnatomicalStructure a owl:Class ; biolink:Haplotype a owl:Class ; rdfs:label "haplotype" ; rdfs:subClassOf [ a owl:Restriction ; + owl:allValuesFrom biolink:OrganismTaxon ; + owl:onProperty biolink:in_taxon ], + [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass biolink:BiologicalSequence ; owl:onProperty biolink:has_biological_sequence ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:OrganismTaxon ; - owl:onProperty biolink:in_taxon ], biolink:BiologicalEntity, biolink:GenomicEntity, biolink:OntologyClass, @@ -956,11 +956,11 @@ biolink:InformationContentEntityToNamedThingAssociation a owl:Class ; owl:qualifiedCardinality 1 ], [ a owl:Restriction ; owl:onClass biolink:NamedThing ; - owl:onProperty rdf:subject ; + owl:onProperty rdf:object ; owl:qualifiedCardinality 1 ], [ a owl:Restriction ; owl:onClass biolink:NamedThing ; - owl:onProperty rdf:object ; + owl:onProperty rdf:subject ; owl:qualifiedCardinality 1 ], biolink:Association ; skos:definition "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)." . @@ -1019,16 +1019,16 @@ biolink:Macronutrient a owl:Class ; biolink:MaterialSampleDerivationAssociation a owl:Class ; rdfs:label "material sample derivation association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:onClass biolink:NamedThing ; - owl:onProperty rdf:object ; + owl:onClass biolink:MaterialSample ; + owl:onProperty rdf:subject ; owl:qualifiedCardinality 1 ], [ a owl:Restriction ; owl:onClass biolink:PredicateType ; owl:onProperty rdf:predicate ; owl:qualifiedCardinality 1 ], [ a owl:Restriction ; - owl:onClass biolink:MaterialSample ; - owl:onProperty rdf:subject ; + owl:onClass biolink:NamedThing ; + owl:onProperty rdf:object ; owl:qualifiedCardinality 1 ], biolink:Association ; skos:definition "An association between a material sample and the material entity from which it is derived." . @@ -1050,13 +1050,13 @@ biolink:MicroRNA a owl:Class ; biolink:MolecularActivityToChemicalEntityAssociation a owl:Class ; rdfs:label "molecular activity to chemical entity association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:onClass biolink:MolecularActivity ; - owl:onProperty rdf:subject ; - owl:qualifiedCardinality 1 ], - [ a owl:Restriction ; owl:onClass biolink:ChemicalEntity ; owl:onProperty rdf:object ; owl:qualifiedCardinality 1 ], + [ a owl:Restriction ; + owl:onClass biolink:MolecularActivity ; + owl:onProperty rdf:subject ; + owl:qualifiedCardinality 1 ], 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" . @@ -1064,11 +1064,11 @@ biolink:MolecularActivityToMolecularActivityAssociation a owl:Class ; rdfs:label "molecular activity to molecular activity association" ; rdfs:subClassOf [ a owl:Restriction ; owl:onClass biolink:MolecularActivity ; - owl:onProperty rdf:subject ; + owl:onProperty rdf:object ; owl:qualifiedCardinality 1 ], [ a owl:Restriction ; owl:onClass biolink:MolecularActivity ; - owl:onProperty rdf:object ; + owl:onProperty rdf:subject ; owl:qualifiedCardinality 1 ], 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" . @@ -1087,10 +1087,6 @@ biolink:NucleicAcidSequenceMotif a owl:Class ; biolink:OrganismTaxonToEnvironmentAssociation a owl:Class ; rdfs:label "organism taxon to environment association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:onClass biolink:PredicateType ; - owl:onProperty rdf:predicate ; - owl:qualifiedCardinality 1 ], - [ a owl:Restriction ; owl:onClass biolink:NamedThing ; owl:onProperty rdf:object ; owl:qualifiedCardinality 1 ], @@ -1098,40 +1094,44 @@ biolink:OrganismTaxonToEnvironmentAssociation a owl:Class ; owl:onClass biolink:OrganismTaxon ; owl:onProperty rdf:subject ; owl:qualifiedCardinality 1 ], + [ a owl:Restriction ; + owl:onClass biolink:PredicateType ; + owl:onProperty rdf:predicate ; + owl:qualifiedCardinality 1 ], biolink:Association, biolink:OrganismTaxonToEntityAssociation . biolink:OrganismTaxonToOrganismTaxonInteraction a owl:Class ; rdfs:label "organism taxon to organism taxon interaction" ; rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty biolink:associated_environmental_context ], - [ a owl:Restriction ; owl:onClass biolink:OrganismTaxon ; owl:onProperty rdf:object ; owl:qualifiedCardinality 1 ], + [ a owl:Restriction ; + owl:onClass biolink:OrganismTaxon ; + owl:onProperty rdf:subject ; + owl:qualifiedCardinality 1 ], [ a owl:Restriction ; owl:onClass biolink:PredicateType ; owl:onProperty rdf:predicate ; owl:qualifiedCardinality 1 ], [ a owl:Restriction ; - owl:onClass biolink:OrganismTaxon ; - owl:onProperty rdf:subject ; - owl:qualifiedCardinality 1 ], + owl:maxQualifiedCardinality 1 ; + owl:onClass linkml:String ; + owl:onProperty biolink:associated_environmental_context ], 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" . biolink:OrganismTaxonToOrganismTaxonSpecialization a owl:Class ; rdfs:label "organism taxon to organism taxon specialization" ; rdfs:subClassOf [ a owl:Restriction ; - owl:onClass biolink:PredicateType ; - owl:onProperty rdf:predicate ; - owl:qualifiedCardinality 1 ], - [ a owl:Restriction ; owl:onClass biolink:OrganismTaxon ; owl:onProperty rdf:subject ; owl:qualifiedCardinality 1 ], + [ a owl:Restriction ; + owl:onClass biolink:PredicateType ; + owl:onProperty rdf:predicate ; + owl:qualifiedCardinality 1 ], [ a owl:Restriction ; owl:onClass biolink:OrganismTaxon ; owl:onProperty rdf:object ; @@ -1145,27 +1145,19 @@ biolink:OrganismToOrganismAssociation a owl:Class ; owl:onClass biolink:IndividualOrganism ; owl:onProperty rdf:object ; owl:qualifiedCardinality 1 ], - [ a owl:Restriction ; - owl:onClass biolink:IndividualOrganism ; - owl:onProperty rdf:subject ; - owl:qualifiedCardinality 1 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass linkml:String ; owl:onProperty biolink:relation ], + [ a owl:Restriction ; + owl:onClass biolink:IndividualOrganism ; + owl:onProperty rdf:subject ; + owl:qualifiedCardinality 1 ], biolink:Association . biolink:OrganismalEntityAsAModelOfDiseaseAssociation a owl:Class ; rdfs:label "organismal entity as a model of disease association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:FrequencyValue ; - owl:onProperty biolink:frequency_qualifier ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:SeverityValue ; - owl:onProperty biolink:severity_qualifier ], - [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass biolink:Onset ; owl:onProperty biolink:onset_qualifier ], @@ -1173,6 +1165,14 @@ biolink:OrganismalEntityAsAModelOfDiseaseAssociation a owl:Class ; owl:onClass biolink:OrganismalEntity ; owl:onProperty rdf:subject ; owl:qualifiedCardinality 1 ], + [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass biolink:FrequencyValue ; + owl:onProperty biolink:frequency_qualifier ], + [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass biolink:SeverityValue ; + owl:onProperty biolink:severity_qualifier ], biolink:Association, biolink:EntityToDiseaseAssociationMixin, biolink:ModelToDiseaseAssociationMixin . @@ -1184,25 +1184,25 @@ biolink:PairwiseMolecularInteraction a owl:Class ; owl:onProperty rdf:predicate ; owl:qualifiedCardinality 1 ], [ a owl:Restriction ; - owl:onClass biolink:MolecularEntity ; - owl:onProperty rdf:object ; - owl:qualifiedCardinality 1 ], - [ a owl:Restriction ; - owl:onClass biolink:MolecularEntity ; - owl:onProperty rdf:subject ; - owl:qualifiedCardinality 1 ], + owl:maxQualifiedCardinality 1 ; + owl:onClass linkml:String ; + owl:onProperty biolink:relation ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass biolink:OntologyClass ; owl:onProperty biolink:interacting_molecules_category ], [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty biolink:relation ], + owl:onClass biolink:MolecularEntity ; + owl:onProperty rdf:object ; + owl:qualifiedCardinality 1 ], [ a owl:Restriction ; owl:onClass linkml:String ; owl:onProperty biolink:id ; owl:qualifiedCardinality 1 ], + [ a owl:Restriction ; + owl:onClass biolink:MolecularEntity ; + owl:onProperty rdf:subject ; + owl:qualifiedCardinality 1 ], biolink:PairwiseGeneToGeneInteraction ; skos:definition "An interaction at the molecular level between two physical entities" . @@ -1303,6 +1303,10 @@ biolink:PhysiologicalProcess a owl:Class ; biolink:PopulationToPopulationAssociation a owl:Class ; rdfs:label "population to population association" ; rdfs:subClassOf [ a owl:Restriction ; + owl:onClass biolink:PredicateType ; + owl:onProperty rdf:predicate ; + owl:qualifiedCardinality 1 ], + [ a owl:Restriction ; owl:onClass biolink:PopulationOfIndividualOrganisms ; owl:onProperty rdf:object ; owl:qualifiedCardinality 1 ], @@ -1310,10 +1314,6 @@ biolink:PopulationToPopulationAssociation a owl:Class ; owl:onClass biolink:PopulationOfIndividualOrganisms ; owl:onProperty rdf:subject ; owl:qualifiedCardinality 1 ], - [ a owl:Restriction ; - owl:onClass biolink:PredicateType ; - owl:onProperty rdf:predicate ; - owl:qualifiedCardinality 1 ], biolink:Association ; skos:definition "An association between a two populations" . @@ -1378,12 +1378,12 @@ biolink:ReactionToCatalystAssociation a owl:Class ; biolink:ReagentTargetedGene a owl:Class ; rdfs:label "reagent targeted gene" ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom biolink:OrganismTaxon ; - owl:onProperty biolink:in_taxon ], - [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass biolink:BiologicalSequence ; owl:onProperty biolink:has_biological_sequence ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:OrganismTaxon ; + owl:onProperty biolink:in_taxon ], biolink:BiologicalEntity, biolink:GenomicEntity, biolink:OntologyClass, @@ -1419,10 +1419,6 @@ biolink:SequenceVariantModulatesTreatmentAssociation a owl:Class ; biolink:Serial a owl:Class ; rdfs:label "serial" ; rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty biolink:volume ], - [ a owl:Restriction ; owl:onClass linkml:String ; owl:onProperty rdf:type ; owl:qualifiedCardinality 1 ], @@ -1431,13 +1427,17 @@ biolink:Serial a owl:Class ; owl:onClass linkml:String ; owl:onProperty biolink:issue ], [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; owl:onClass linkml:String ; - owl:onProperty biolink:id ; - owl:qualifiedCardinality 1 ], + owl:onProperty biolink:iso_abbreviation ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass linkml:String ; - owl:onProperty biolink:iso_abbreviation ], + owl:onProperty biolink:volume ], + [ a owl:Restriction ; + owl:onClass linkml:String ; + owl:onProperty biolink:id ; + owl:qualifiedCardinality 1 ], 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." . @@ -1497,7 +1497,7 @@ biolink:TaxonToTaxonAssociation a owl:Class ; rdfs:label "taxon to taxon association" ; rdfs:subClassOf [ a owl:Restriction ; owl:onClass biolink:OrganismTaxon ; - owl:onProperty rdf:object ; + owl:onProperty rdf:subject ; owl:qualifiedCardinality 1 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; @@ -1505,7 +1505,7 @@ biolink:TaxonToTaxonAssociation a owl:Class ; owl:onProperty biolink:relation ], [ a owl:Restriction ; owl:onClass biolink:OrganismTaxon ; - owl:onProperty rdf:subject ; + owl:onProperty rdf:object ; owl:qualifiedCardinality 1 ], biolink:Association . @@ -1541,9 +1541,17 @@ biolink:VariantAsAModelOfDiseaseAssociation a owl:Class ; biolink:VariantToGeneExpressionAssociation a owl:Class ; rdfs:label "variant to gene expression association" ; rdfs:subClassOf [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass biolink:AnatomicalEntity ; + owl:onProperty biolink:expression_site ], + [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass biolink:DiseaseOrPhenotypicFeature ; owl:onProperty biolink:phenotypic_state ], + [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass biolink:LifeStage ; + owl:onProperty biolink:stage_qualifier ], [ a owl:Restriction ; owl:onClass biolink:PredicateType ; owl:onProperty rdf:predicate ; @@ -1552,14 +1560,6 @@ biolink:VariantToGeneExpressionAssociation a owl:Class ; owl:maxQualifiedCardinality 1 ; owl:onClass biolink:OntologyClass ; owl:onProperty biolink:quantifier_qualifier ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:LifeStage ; - owl:onProperty biolink:stage_qualifier ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:AnatomicalEntity ; - owl:onProperty biolink:expression_site ], biolink:GeneExpressionMixin, biolink:VariantToGeneAssociation ; skos:definition "An association between a variant and expression of a gene (i.e. e-QTL)" . @@ -1568,24 +1568,24 @@ biolink:VariantToPhenotypicFeatureAssociation a owl:Class ; rdfs:label "variant to phenotypic feature association" ; rdfs:subClassOf [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:Onset ; - owl:onProperty biolink:onset_qualifier ], + owl:onClass biolink:BiologicalSex ; + owl:onProperty biolink:sex_qualifier ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:SeverityValue ; - owl:onProperty biolink:severity_qualifier ], + owl:onClass biolink:FrequencyValue ; + owl:onProperty biolink:frequency_qualifier ], + [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass biolink:Onset ; + owl:onProperty biolink:onset_qualifier ], [ a owl:Restriction ; owl:onClass biolink:SequenceVariant ; owl:onProperty rdf:subject ; owl:qualifiedCardinality 1 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:BiologicalSex ; - owl:onProperty biolink:sex_qualifier ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:FrequencyValue ; - owl:onProperty biolink:frequency_qualifier ], + owl:onClass biolink:SeverityValue ; + owl:onProperty biolink:severity_qualifier ], biolink:Association, biolink:EntityToPhenotypicFeatureAssociationMixin, biolink:VariantToEntityAssociationMixin . @@ -1594,12 +1594,8 @@ biolink:VariantToPopulationAssociation a owl:Class ; rdfs:label "variant to population association" ; rdfs:subClassOf [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:Double ; - owl:onProperty biolink:has_quotient ], - [ a owl:Restriction ; - owl:onClass biolink:PopulationOfIndividualOrganisms ; - owl:onProperty rdf:object ; - owl:qualifiedCardinality 1 ], + owl:onClass linkml:Integer ; + owl:onProperty biolink:has_total ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass biolink:FrequencyValue ; @@ -1615,11 +1611,15 @@ biolink:VariantToPopulationAssociation a owl:Class ; [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass linkml:Integer ; - owl:onProperty biolink:has_total ], + owl:onProperty biolink:has_count ], + [ a owl:Restriction ; + owl:onClass biolink:PopulationOfIndividualOrganisms ; + owl:onProperty rdf:object ; + owl:qualifiedCardinality 1 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:Integer ; - owl:onProperty biolink:has_count ], + owl:onClass linkml:Double ; + owl:onProperty biolink:has_quotient ], biolink:Association, biolink:FrequencyQualifierMixin, biolink:FrequencyQuantifier, @@ -1712,14 +1712,6 @@ biolink:clinical_modifier_qualifier a owl:ObjectProperty ; rdfs:subPropertyOf biolink:association_slot ; skos:definition "Used to characterize and specify the phenotypic abnormalities defined in the Phenotypic abnormality subontology, with respect to severity, laterality, age of onset, and other aspects" . -biolink:co_occurs_in_literature_with a owl:ObjectProperty, - owl:SymmetricProperty ; - rdfs:label "co-occurs in literature with" ; - rdfs:domain biolink:NamedThing ; - rdfs:range biolink:NamedThing ; - rdfs:subPropertyOf biolink:correlated_with ; - skos:definition "holds between two entities where their co-occurrence is correlated by counts of publications in which both occur, using some threshold of occurrence as defined by the edge provider." . - biolink:coexpressed_with a owl:ObjectProperty, owl:SymmetricProperty ; rdfs:label "coexpressed with" ; @@ -1925,6 +1917,14 @@ biolink:negatively_correlated_with a owl:ObjectProperty, rdfs:subPropertyOf biolink:correlated_with ; skos:definition "holds between any two named thing entities \"correlated with\" one another in a negative manner." . +biolink:occurs_together_in_literature_with a owl:ObjectProperty, + owl:SymmetricProperty ; + rdfs:label "occurs together in literature with" ; + rdfs:domain biolink:NamedThing ; + rdfs:range biolink:NamedThing ; + rdfs:subPropertyOf biolink:correlated_with ; + skos:definition "holds between two entities where their co-occurrence is correlated by counts of publications in which both occur, using some threshold of occurrence as defined by the edge provider." . + biolink:opposite_of a owl:ObjectProperty, owl:SymmetricProperty ; rdfs:label "opposite of" ; @@ -2139,17 +2139,17 @@ biolink:BehavioralFeature a owl:Class ; biolink:BookChapter a owl:Class ; rdfs:label "book chapter" ; rdfs:subClassOf [ a owl:Restriction ; - owl:onClass linkml:Uriorcurie ; - owl:onProperty biolink:published_in ; - owl:qualifiedCardinality 1 ], - [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass linkml:String ; - owl:onProperty biolink:volume ], + owl:onProperty biolink:chapter ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass linkml:String ; - owl:onProperty biolink:chapter ], + owl:onProperty biolink:volume ], + [ a owl:Restriction ; + owl:onClass linkml:Uriorcurie ; + owl:onProperty biolink:published_in ; + owl:qualifiedCardinality 1 ], biolink:Publication . biolink:Case a owl:Class ; @@ -2268,50 +2268,50 @@ biolink:Exon a owl:Class ; biolink:FrequencyQuantifier a owl:Class ; rdfs:label "frequency quantifier" ; rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:Double ; - owl:onProperty biolink:has_quotient ], - [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass linkml:Integer ; owl:onProperty biolink:has_total ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:Integer ; - owl:onProperty biolink:has_count ], + owl:onClass linkml:Double ; + owl:onProperty biolink:has_percentage ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass linkml:Double ; - owl:onProperty biolink:has_percentage ], + owl:onProperty biolink:has_quotient ], + [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass linkml:Integer ; + owl:onProperty biolink:has_count ], biolink:RelationshipQuantifier, linkml:mixin . biolink:GenotypeToDiseaseAssociation a owl:Class ; rdfs:label "genotype to disease association" ; rdfs:subClassOf [ a owl:Restriction ; + owl:onClass biolink:PredicateType ; + owl:onProperty rdf:predicate ; + owl:qualifiedCardinality 1 ], + [ a owl:Restriction ; owl:onClass biolink:NamedThing ; owl:onProperty rdf:subject ; owl:qualifiedCardinality 1 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:SeverityValue ; - owl:onProperty biolink:severity_qualifier ], + owl:onClass biolink:FrequencyValue ; + owl:onProperty biolink:frequency_qualifier ], [ a owl:Restriction ; owl:onClass biolink:NamedThing ; owl:onProperty rdf:object ; owl:qualifiedCardinality 1 ], - [ a owl:Restriction ; - owl:onClass biolink:PredicateType ; - owl:onProperty rdf:predicate ; - owl:qualifiedCardinality 1 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass biolink:Onset ; owl:onProperty biolink:onset_qualifier ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:FrequencyValue ; - owl:onProperty biolink:frequency_qualifier ], + owl:onClass biolink:SeverityValue ; + owl:onProperty biolink:severity_qualifier ], biolink:Association, biolink:EntityToDiseaseAssociationMixin, biolink:GenotypeToEntityAssociationMixin ; @@ -2345,13 +2345,13 @@ biolink:MolecularMixture a owl:Class ; biolink:PairwiseGeneToGeneInteraction a owl:Class ; rdfs:label "pairwise gene to gene interaction" ; rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty biolink:relation ], - [ a owl:Restriction ; owl:onClass biolink:PredicateType ; owl:onProperty rdf:predicate ; owl:qualifiedCardinality 1 ], + [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass linkml:String ; + owl:onProperty biolink:relation ], 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)" . @@ -2382,14 +2382,6 @@ biolink:Polypeptide a owl:Class ; biolink:ReactionToParticipantAssociation a owl:Class ; rdfs:label "reaction to participant association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass ; - owl:onProperty biolink:reaction_direction ], - [ a owl:Restriction ; - owl:onClass biolink:MolecularEntity ; - owl:onProperty rdf:subject ; - owl:qualifiedCardinality 1 ], - [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass linkml:Integer ; owl:onProperty biolink:stoichiometry ], @@ -2397,6 +2389,14 @@ biolink:ReactionToParticipantAssociation a owl:Class ; owl:maxQualifiedCardinality 1 ; owl:onClass ; owl:onProperty biolink:reaction_side ], + [ a owl:Restriction ; + owl:onClass biolink:MolecularEntity ; + owl:onProperty rdf:subject ; + owl:qualifiedCardinality 1 ], + [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass ; + owl:onProperty biolink:reaction_direction ], biolink:ChemicalToChemicalAssociation . biolink:SequenceAssociation a owl:Class ; @@ -2428,15 +2428,15 @@ biolink:TaxonomicRank a owl:Class ; biolink:Treatment a owl:Class ; rdfs:label "treatment" ; rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:TimeType ; - owl:onProperty biolink:timepoint ], - [ a owl:Restriction ; owl:allValuesFrom biolink:Procedure ; owl:onProperty biolink:has_procedure ], [ a owl:Restriction ; owl:allValuesFrom biolink:Device ; owl:onProperty biolink:has_device ], + [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass biolink:TimeType ; + owl:onProperty biolink:timepoint ], [ a owl:Restriction ; owl:allValuesFrom biolink:Drug ; owl:onProperty biolink:has_drug ], @@ -2453,29 +2453,29 @@ biolink:Treatment a owl:Class ; biolink:VariantToDiseaseAssociation a owl:Class ; rdfs:label "variant to disease association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:onClass biolink:NamedThing ; - owl:onProperty rdf:object ; - owl:qualifiedCardinality 1 ], - [ a owl:Restriction ; - owl:onClass biolink:NamedThing ; - owl:onProperty rdf:subject ; - owl:qualifiedCardinality 1 ], - [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass biolink:FrequencyValue ; owl:onProperty biolink:frequency_qualifier ], + [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass biolink:Onset ; + owl:onProperty biolink:onset_qualifier ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass biolink:SeverityValue ; owl:onProperty biolink:severity_qualifier ], + [ a owl:Restriction ; + owl:onClass biolink:NamedThing ; + owl:onProperty rdf:subject ; + owl:qualifiedCardinality 1 ], + [ a owl:Restriction ; + owl:onClass biolink:NamedThing ; + owl:onProperty rdf:object ; + owl:qualifiedCardinality 1 ], [ a owl:Restriction ; owl:onClass biolink:PredicateType ; owl:onProperty rdf:predicate ; owl:qualifiedCardinality 1 ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:Onset ; - owl:onProperty biolink:onset_qualifier ], biolink:Association, biolink:EntityToDiseaseAssociationMixin, biolink:VariantToEntityAssociationMixin ; @@ -2484,13 +2484,13 @@ biolink:VariantToDiseaseAssociation a owl:Class ; biolink:VariantToGeneAssociation a owl:Class ; rdfs:label "variant to gene association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:onClass biolink:Gene ; - owl:onProperty rdf:object ; - owl:qualifiedCardinality 1 ], - [ a owl:Restriction ; owl:onClass biolink:PredicateType ; owl:onProperty rdf:predicate ; owl:qualifiedCardinality 1 ], + [ a owl:Restriction ; + owl:onClass biolink:Gene ; + owl:onProperty rdf:object ; + owl:qualifiedCardinality 1 ], biolink:Association, biolink:VariantToEntityAssociationMixin ; 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)" . @@ -4272,11 +4272,11 @@ biolink:AnatomicalEntityToAnatomicalEntityAssociation a owl:Class ; rdfs:label "anatomical entity to anatomical entity association" ; rdfs:subClassOf [ a owl:Restriction ; owl:onClass biolink:AnatomicalEntity ; - owl:onProperty rdf:subject ; + owl:onProperty rdf:object ; owl:qualifiedCardinality 1 ], [ a owl:Restriction ; owl:onClass biolink:AnatomicalEntity ; - owl:onProperty rdf:object ; + owl:onProperty rdf:subject ; owl:qualifiedCardinality 1 ], biolink:Association . @@ -4413,20 +4413,20 @@ biolink:GeneToDiseaseAssociation a owl:Class ; rdfs:label "gene to disease association" ; rdfs:subClassOf [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:FrequencyValue ; - owl:onProperty biolink:frequency_qualifier ], + owl:onClass biolink:Onset ; + owl:onProperty biolink:onset_qualifier ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass biolink:SeverityValue ; owl:onProperty biolink:severity_qualifier ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:Onset ; - owl:onProperty biolink:onset_qualifier ], [ a owl:Restriction ; owl:onClass biolink:GeneOrGeneProduct ; owl:onProperty rdf:subject ; owl:qualifiedCardinality 1 ], + [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass biolink:FrequencyValue ; + owl:onProperty biolink:frequency_qualifier ], biolink:Association, biolink:EntityToDiseaseAssociationMixin, biolink:GeneToEntityAssociationMixin ; @@ -4504,11 +4504,11 @@ biolink:Procedure a owl:Class ; biolink:RNAProduct a owl:Class ; rdfs:label "RNA product" ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom linkml:Uriorcurie ; - owl:onProperty biolink:xref ], - [ a owl:Restriction ; owl:allValuesFrom biolink:LabelType ; owl:onProperty biolink:synonym ], + [ a owl:Restriction ; + owl:allValuesFrom linkml:Uriorcurie ; + owl:onProperty biolink:xref ], biolink:GeneProductMixin, biolink:Transcript ; skos:exactMatch , @@ -4776,26 +4776,30 @@ biolink:DiseaseToEntityAssociationMixin a owl:Class ; biolink:Entity a owl:Class ; rdfs:label "entity" ; rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; owl:onClass linkml:String ; - owl:onProperty rdf:type ], + owl:onProperty biolink:id ; + owl:qualifiedCardinality 1 ], [ a owl:Restriction ; owl:allValuesFrom biolink:Agent ; owl:onProperty biolink:provided_by ], [ a owl:Restriction ; owl:allValuesFrom biolink:CategoryType ; owl:onProperty biolink:category ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:LabelType ; - owl:onProperty biolink:source ], [ a owl:Restriction ; owl:allValuesFrom biolink:Attribute ; owl:onProperty biolink:has_attribute ], [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass biolink:LabelType ; + owl:onProperty rdfs:label ], + [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; owl:onClass linkml:String ; - owl:onProperty biolink:id ; - owl:qualifiedCardinality 1 ], + owl:onProperty rdf:type ], + [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass biolink:LabelType ; + owl:onProperty biolink:source ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass biolink:NarrativeText ; @@ -4803,11 +4807,7 @@ biolink:Entity a owl:Class ; [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass biolink:IriType ; - owl:onProperty biolink:iri ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:LabelType ; - owl:onProperty rdfs:label ] ; + owl:onProperty biolink:iri ] ; skos:definition "Root Biolink Model class for all things and informational relationships, real or imagined." . biolink:FrequencyQualifierMixin a owl:Class ; @@ -4829,14 +4829,14 @@ biolink:GeneExpressionMixin a owl:Class ; owl:maxQualifiedCardinality 1 ; owl:onClass biolink:OntologyClass ; owl:onProperty biolink:quantifier_qualifier ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:DiseaseOrPhenotypicFeature ; - owl:onProperty biolink:phenotypic_state ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass biolink:AnatomicalEntity ; owl:onProperty biolink:expression_site ], + [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass biolink:DiseaseOrPhenotypicFeature ; + owl:onProperty biolink:phenotypic_state ], linkml:mixin ; skos:definition "Observed gene expression intensity, context (site, stage) and associated phenotypic status within which the expression occurs." . @@ -5324,13 +5324,13 @@ biolink:ClinicalAttribute a owl:Class ; biolink:DatasetVersion a owl:Class ; rdfs:label "dataset version" ; rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty pav:version ], - [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass biolink:Dataset ; owl:onProperty dct:source ], + [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass linkml:String ; + owl:onProperty pav:version ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass biolink:DatasetDistribution ; @@ -5369,13 +5369,13 @@ biolink:EntityToDiseaseOrPhenotypicFeatureAssociationMixin a owl:Class ; biolink:FunctionalAssociation a owl:Class ; rdfs:label "functional association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:onClass biolink:GeneOntologyClass ; - owl:onProperty rdf:object ; - owl:qualifiedCardinality 1 ], - [ a owl:Restriction ; owl:onClass biolink:MacromolecularMachineMixin ; owl:onProperty rdf:subject ; owl:qualifiedCardinality 1 ], + [ a owl:Restriction ; + owl:onClass biolink:GeneOntologyClass ; + owl:onProperty rdf:object ; + owl:qualifiedCardinality 1 ], 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." . @@ -5557,6 +5557,10 @@ biolink:xref a owl:ObjectProperty ; biolink:ChemicalMixture a owl:Class ; rdfs:label "chemical mixture" ; rdfs:subClassOf [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass linkml:String ; + owl:onProperty biolink:highest_FDA_approval_status ], + [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass linkml:String ; owl:onProperty biolink:drug_regulatory_status_world_wide ], @@ -5564,10 +5568,6 @@ biolink:ChemicalMixture a owl:Class ; owl:maxQualifiedCardinality 1 ; owl:onClass biolink:ChemicalMixture ; owl:onProperty biolink:is_supplement ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty biolink:highest_FDA_approval_status ], biolink:ChemicalEntity ; skos:definition "A chemical mixture is a chemical entity composed of two or more molecular entities." . @@ -5582,11 +5582,11 @@ biolink:GeneGroupingMixin a owl:Class ; biolink:GeneProductMixin a owl:Class ; rdfs:label "gene product mixin" ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom linkml:Uriorcurie ; - owl:onProperty biolink:xref ], - [ a owl:Restriction ; owl:allValuesFrom biolink:LabelType ; owl:onProperty biolink:synonym ], + [ a owl:Restriction ; + owl:allValuesFrom linkml:Uriorcurie ; + owl:onProperty biolink:xref ], biolink:GeneOrGeneProduct, linkml:mixin ; skos:definition "The functional molecular product of a single gene locus. Gene products are either proteins or functional RNA molecules." ; @@ -5670,10 +5670,6 @@ biolink:part_of a owl:ObjectProperty ; biolink:EntityToPhenotypicFeatureAssociationMixin a owl:Class ; rdfs:label "entity to phenotypic feature association mixin" ; rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:NarrativeText ; - owl:onProperty dct:description ], - [ a owl:Restriction ; owl:onClass biolink:PhenotypicFeature ; owl:onProperty rdf:object ; owl:qualifiedCardinality 1 ], @@ -5681,22 +5677,26 @@ biolink:EntityToPhenotypicFeatureAssociationMixin a owl:Class ; owl:maxQualifiedCardinality 1 ; owl:onClass biolink:BiologicalSex ; owl:onProperty biolink:sex_qualifier ], + [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass biolink:NarrativeText ; + owl:onProperty dct:description ], biolink:EntityToFeatureOrDiseaseQualifiersMixin, linkml:mixin . biolink:Genotype a owl:Class ; rdfs:label "genotype" ; rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:Zygosity ; - owl:onProperty biolink:has_zygosity ], - [ a owl:Restriction ; owl:allValuesFrom biolink:OrganismTaxon ; owl:onProperty biolink:in_taxon ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass biolink:BiologicalSequence ; owl:onProperty biolink:has_biological_sequence ], + [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass biolink:Zygosity ; + owl:onProperty biolink:has_zygosity ], biolink:BiologicalEntity, biolink:GenomicEntity, biolink:OntologyClass, @@ -5756,10 +5756,10 @@ biolink:MolecularActivity a owl:Class ; owl:onProperty biolink:enabled_by ], [ a owl:Restriction ; owl:allValuesFrom biolink:MolecularEntity ; - owl:onProperty biolink:has_input ], + owl:onProperty biolink:has_output ], [ a owl:Restriction ; owl:allValuesFrom biolink:MolecularEntity ; - owl:onProperty biolink:has_output ], + owl:onProperty biolink:has_input ], biolink:BiologicalProcessOrActivity, biolink:Occurrent, biolink:OntologyClass ; @@ -5803,14 +5803,14 @@ biolink:Agent a owl:Class ; owl:onClass linkml:String ; owl:onProperty biolink:id ; owl:qualifiedCardinality 1 ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:LabelType ; - owl:onProperty rdfs:label ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass linkml:String ; owl:onProperty biolink:address ], + [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass biolink:LabelType ; + owl:onProperty rdfs:label ], biolink:AdministrativeEntity ; skos:altLabel "group" ; skos:definition "person, group, organization or project that provides a piece of information (i.e. a knowledge association)" ; @@ -5826,11 +5826,11 @@ biolink:Agent a owl:Class ; biolink:BiologicalProcessOrActivity a owl:Class ; rdfs:label "biological process or activity" ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom biolink:BiologicalProcessOrActivity ; - owl:onProperty biolink:has_input ], - [ a owl:Restriction ; owl:allValuesFrom biolink:PhysicalEntity ; owl:onProperty biolink:enabled_by ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:BiologicalProcessOrActivity ; + owl:onProperty biolink:has_input ], [ a owl:Restriction ; owl:allValuesFrom biolink:BiologicalProcessOrActivity ; owl:onProperty biolink:has_output ], @@ -5852,30 +5852,30 @@ biolink:GenomicSequenceLocalization a owl:Class ; [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass linkml:Integer ; - owl:onProperty biolink:start_interbase_coordinate ], + owl:onProperty biolink:end_interbase_coordinate ], [ a owl:Restriction ; owl:onClass biolink:NucleicAcidEntity ; - owl:onProperty rdf:subject ; + owl:onProperty rdf:object ; owl:qualifiedCardinality 1 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass linkml:Integer ; - owl:onProperty biolink:end_interbase_coordinate ], + owl:onProperty biolink:start_interbase_coordinate ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass ; - owl:onProperty biolink:phase ], + owl:onClass ; + owl:onProperty biolink:genome_build ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass ; owl:onProperty biolink:strand ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass ; - owl:onProperty biolink:genome_build ], + owl:onClass ; + owl:onProperty biolink:phase ], [ a owl:Restriction ; owl:onClass biolink:NucleicAcidEntity ; - owl:onProperty rdf:object ; + owl:onProperty rdf:subject ; owl:qualifiedCardinality 1 ], biolink:SequenceAssociation ; 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." . @@ -5885,17 +5885,20 @@ biolink:has_biological_sequence a owl:ObjectProperty . biolink:Attribute a owl:Class ; rdfs:label "attribute" ; rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:LabelType ; - owl:onProperty biolink:source ], - [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass biolink:NamedThing ; owl:onProperty biolink:has_qualitative_value ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:QuantityValue ; + owl:onProperty biolink:has_quantitative_value ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass biolink:IriType ; owl:onProperty biolink:iri ], + [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass biolink:LabelType ; + owl:onProperty biolink:source ], [ a owl:Restriction ; owl:onClass biolink:OntologyClass ; owl:onProperty biolink:has_attribute_type ; @@ -5904,9 +5907,6 @@ biolink:Attribute a owl:Class ; owl:maxQualifiedCardinality 1 ; owl:onClass biolink:LabelType ; owl:onProperty rdfs:label ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:QuantityValue ; - owl:onProperty biolink:has_quantitative_value ], biolink:Annotation, biolink:OntologyClass ; 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." ; @@ -5983,7 +5983,7 @@ biolink:InformationContentEntity a owl:Class ; rdfs:subClassOf [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass linkml:String ; - owl:onProperty biolink:license ], + owl:onProperty biolink:rights ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass linkml:String ; @@ -5995,7 +5995,7 @@ biolink:InformationContentEntity a owl:Class ; [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass linkml:String ; - owl:onProperty biolink:rights ], + owl:onProperty biolink:license ], biolink:NamedThing ; skos:altLabel "information", "information artefact", @@ -6055,27 +6055,27 @@ biolink:Publication a owl:Class ; [ a owl:Restriction ; owl:allValuesFrom linkml:Uriorcurie ; owl:onProperty biolink:mesh_terms ], + [ a owl:Restriction ; + owl:allValuesFrom linkml:String ; + owl:onProperty biolink:keywords ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass linkml:String ; owl:onProperty biolink:summary ], [ a owl:Restriction ; owl:allValuesFrom linkml:String ; - owl:onProperty biolink:pages ], + owl:onProperty biolink:authors ], [ a owl:Restriction ; owl:allValuesFrom linkml:String ; - owl:onProperty biolink:keywords ], + owl:onProperty biolink:pages ], [ a owl:Restriction ; owl:onClass linkml:String ; - owl:onProperty biolink:id ; + owl:onProperty dct:type ; owl:qualifiedCardinality 1 ], [ a owl:Restriction ; owl:onClass linkml:String ; - owl:onProperty dct:type ; + owl:onProperty biolink:id ; owl:qualifiedCardinality 1 ], - [ a owl:Restriction ; - owl:allValuesFrom linkml:String ; - owl:onProperty biolink:authors ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass biolink:LabelType ; @@ -6190,9 +6190,6 @@ biolink:SequenceVariant a owl:Class ; owl:maxQualifiedCardinality 1 ; owl:onClass biolink:BiologicalSequence ; owl:onProperty biolink:has_biological_sequence ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:Gene ; - owl:onProperty biolink:has_gene ], [ a owl:Restriction ; owl:onClass linkml:String ; owl:onProperty biolink:id ; @@ -6200,6 +6197,9 @@ biolink:SequenceVariant a owl:Class ; [ a owl:Restriction ; owl:allValuesFrom biolink:OrganismTaxon ; owl:onProperty biolink:in_taxon ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:Gene ; + owl:onProperty biolink:has_gene ], biolink:BiologicalEntity, biolink:GenomicEntity, biolink:OntologyClass, @@ -6217,20 +6217,20 @@ biolink:SequenceVariant a owl:Class ; biolink:ChemicalEntity a owl:Class ; rdfs:label "chemical entity" ; rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:Boolean ; - owl:onProperty biolink:is_toxic ], - [ a owl:Restriction ; - owl:allValuesFrom ; - owl:onProperty biolink:available_from ], - [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass linkml:String ; owl:onProperty biolink:max_tolerated_dose ], + [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass linkml:Boolean ; + owl:onProperty biolink:is_toxic ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass biolink:ChemicalEntity ; owl:onProperty biolink:trade_name ], + [ a owl:Restriction ; + owl:allValuesFrom ; + owl:onProperty biolink:available_from ], biolink:ChemicalEntityOrGeneOrGeneProduct, biolink:ChemicalEntityOrProteinOrPolypeptide, biolink:ChemicalOrDrugOrTreatment, @@ -6311,6 +6311,13 @@ biolink:Gene a owl:Class ; rdfs:subClassOf [ a owl:Restriction ; owl:allValuesFrom linkml:Uriorcurie ; owl:onProperty biolink:xref ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:LabelType ; + owl:onProperty biolink:synonym ], + [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass linkml:String ; + owl:onProperty biolink:symbol ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass biolink:BiologicalSequence ; @@ -6318,13 +6325,6 @@ biolink:Gene a owl:Class ; [ a owl:Restriction ; owl:allValuesFrom biolink:OrganismTaxon ; owl:onProperty biolink:in_taxon ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty biolink:symbol ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:LabelType ; - owl:onProperty biolink:synonym ], biolink:BiologicalEntity, biolink:ChemicalEntityOrGeneOrGeneProduct, biolink:GeneOrGeneProduct, @@ -6383,40 +6383,40 @@ biolink:related_to_at_instance_level a owl:ObjectProperty, biolink:Association a owl:Class ; rdfs:label "association" ; rdfs:subClassOf [ a owl:Restriction ; + owl:onClass biolink:NamedThing ; + owl:onProperty rdf:subject ; + owl:qualifiedCardinality 1 ], + [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass linkml:Boolean ; owl:onProperty biolink:negated ], - [ a owl:Restriction ; - owl:onClass biolink:NamedThing ; - owl:onProperty rdf:object ; - owl:qualifiedCardinality 1 ], [ a owl:Restriction ; owl:allValuesFrom biolink:CategoryType ; owl:onProperty biolink:category ], [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty rdf:type ], + owl:onClass biolink:PredicateType ; + owl:onProperty rdf:predicate ; + owl:qualifiedCardinality 1 ], [ a owl:Restriction ; - owl:allValuesFrom biolink:Publication ; - owl:onProperty biolink:publications ], + owl:allValuesFrom biolink:OntologyClass ; + owl:onProperty biolink:qualifiers ], [ a owl:Restriction ; owl:allValuesFrom biolink:EvidenceType ; owl:onProperty biolink:has_evidence ], [ a owl:Restriction ; - owl:onClass biolink:PredicateType ; - owl:onProperty rdf:predicate ; - owl:qualifiedCardinality 1 ], + owl:allValuesFrom biolink:Publication ; + owl:onProperty biolink:publications ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass linkml:String ; - owl:onProperty biolink:relation ], + owl:onProperty rdf:type ], [ a owl:Restriction ; - owl:allValuesFrom biolink:OntologyClass ; - owl:onProperty biolink:qualifiers ], + owl:maxQualifiedCardinality 1 ; + owl:onClass linkml:String ; + owl:onProperty biolink:relation ], [ a owl:Restriction ; owl:onClass biolink:NamedThing ; - owl:onProperty rdf:subject ; + owl:onProperty rdf:object ; owl:qualifiedCardinality 1 ], biolink:Entity ; skos:definition "A typed association between two entities, supported by evidence" ; diff --git a/biolink-model.ttl b/biolink-model.ttl index 0ddc086722..76fc6262a6 100644 --- a/biolink-model.ttl +++ b/biolink-model.ttl @@ -299,242 +299,242 @@ , , ; - linkml:generation_date "2021-11-08T21:40:25"^^xsd:dateTime ; + linkml:generation_date "2021-11-08T22:05:13"^^xsd:dateTime ; linkml:id ; linkml:imports linkml:types ; linkml:metamodel_version "1.7.0" ; - linkml:prefixes [ linkml:prefix_prefix "OBAN" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "prov" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "biolink" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "NLMID" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "CID" ; - linkml:prefix_reference ], + linkml:prefixes [ linkml:prefix_prefix "EDAM-OPERATION" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "METANETX.REACTION" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "UO-PROPERTY" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "NCBIGene" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "WBVocab" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "ExO" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "CAID" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "UBERGRAPH" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "OBOREL" ; + linkml:prefix_reference ], [ linkml:prefix_prefix "gtpo" ; linkml:prefix_reference ], - [ linkml:prefix_prefix "PDQ" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "isbn" ; - linkml:prefix_reference ], + [ linkml:prefix_prefix "HCPCS" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "GSID" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "PANTHER.FAMILY" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "RXNORM" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "oboformat" ; + linkml:prefix_reference OIO: ], + [ linkml:prefix_prefix "KEGG.RCLASS" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "RXCUI" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "NLMID" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "ICD0" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "linkml" ; + linkml:prefix_reference linkml: ], + [ linkml:prefix_prefix "CHEMBL.MECHANISM" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "prov" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "REPODB" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "pav" ; + linkml:prefix_reference pav: ], + [ linkml:prefix_prefix "Aeolus" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "ORPHA" ; + linkml:prefix_reference ], [ linkml:prefix_prefix "issn" ; linkml:prefix_reference ], + [ linkml:prefix_prefix "FYPO" ; + linkml:prefix_reference ], [ linkml:prefix_prefix "NCIT-OBO" ; linkml:prefix_reference ], - [ linkml:prefix_prefix "hetio" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "foaf" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "chembio" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "bioschemas" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "MI" ; - linkml:prefix_reference ], + [ linkml:prefix_prefix "VANDF" ; + linkml:prefix_reference ], [ linkml:prefix_prefix "KEGG.ENZYME" ; linkml:prefix_reference ], - [ linkml:prefix_prefix "os" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "foodb.compound" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "MetaCyc" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "SEMMEDDB" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "PathWhiz" ; - linkml:prefix_reference ], + [ linkml:prefix_prefix "biolink" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "GAMMA" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "MESH" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "PDQ" ; + linkml:prefix_reference ], [ linkml:prefix_prefix "KEGG.GENE" ; linkml:prefix_reference ], - [ linkml:prefix_prefix "EDAM-DATA" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "XPO" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "Aeolus" ; - linkml:prefix_reference ], + [ linkml:prefix_prefix "MI" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "NDDF" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "dcat" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "bioschemas" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "ICD9" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "MetaCyc" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "COG" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "os" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "isni" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "WIKIDATA" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "MSigDB" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "isbn" ; + linkml:prefix_reference ], [ linkml:prefix_prefix "COAR_RESOURCE" ; linkml:prefix_reference ], - [ linkml:prefix_prefix "GTEx" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "UO-PROPERTY" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "pav" ; - linkml:prefix_reference pav: ], + [ linkml:prefix_prefix "UBERON_NONAMESPACE" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "CID" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "KEGG.PATHWAY" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "mirbase" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "SNPEFF" ; + linkml:prefix_reference ], [ linkml:prefix_prefix "GTOPDB" ; linkml:prefix_reference ], - [ linkml:prefix_prefix "OBOREL" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "GOP" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "STY" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "EDAM-TOPIC" ; - linkml:prefix_reference ], + [ linkml:prefix_prefix "chembio" ; + linkml:prefix_reference ], [ linkml:prefix_prefix "VMC" ; linkml:prefix_reference ], - [ linkml:prefix_prefix "EFO" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "gpi" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "dct" ; - linkml:prefix_reference dcterms: ], - [ linkml:prefix_prefix "ORPHA" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "SIO" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "CTD" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "ORCID" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "EDAM-FORMAT" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "ICD9" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "EDAM-OPERATION" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "COG" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "PANTHER.FAMILY" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "doi" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "VANDF" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "CAID" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "wgs" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "alliancegenome" ; - linkml:prefix_reference ], + [ linkml:prefix_prefix "ResearchID" ; + linkml:prefix_reference ], [ linkml:prefix_prefix "ECTO" ; linkml:prefix_reference ], + [ linkml:prefix_prefix "foaf" ; + linkml:prefix_reference ], [ linkml:prefix_prefix "SEED.REACTION" ; linkml:prefix_reference ], - [ linkml:prefix_prefix "RO" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "CHADO" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "WIKIDATA_PROPERTY" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "UBERON_NONAMESPACE" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "NDDF" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "medgen" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "GAMMA" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "UMLSSG" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "linkml" ; - linkml:prefix_reference linkml: ], - [ linkml:prefix_prefix "GSID" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "ResearchID" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "isni" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "apollo" ; - linkml:prefix_reference ], + [ linkml:prefix_prefix "qud" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "SEMMEDDB" ; + linkml:prefix_reference ], [ linkml:prefix_prefix "GOREL" ; linkml:prefix_reference ], - [ linkml:prefix_prefix "WIKIDATA" ; - linkml:prefix_reference ], + [ linkml:prefix_prefix "SIO" ; + linkml:prefix_reference ], [ linkml:prefix_prefix "CPT" ; linkml:prefix_reference ], - [ linkml:prefix_prefix "qud" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "RXNORM" ; - linkml:prefix_reference ], + [ linkml:prefix_prefix "CLINVAR" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "ChemBank" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "HsapDv" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "RO" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "WIKIDATA_PROPERTY" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "GTEx" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "gpi" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "CTD" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "CHADO" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "EFO" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "doi" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "KEGG.BRITE" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "RTXKG1" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "SNOMED" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "OBAN" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "MAXO" ; + linkml:prefix_reference ], [ linkml:prefix_prefix "DrugCentral" ; linkml:prefix_reference ], - [ linkml:prefix_prefix "REPODB" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "dcat" ; - linkml:prefix_reference ], + [ linkml:prefix_prefix "EDAM-FORMAT" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "apollo" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "SNOMEDCT" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "INO" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "NBO-PROPERTY" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "EDAM-DATA" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "dct" ; + linkml:prefix_reference dcterms: ], [ linkml:prefix_prefix "DOID-PROPERTY" ; linkml:prefix_reference ], - [ linkml:prefix_prefix "gff3" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "WBVocab" ; - linkml:prefix_reference ], + [ linkml:prefix_prefix "UMLSSG" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "KEGG.DGROUP" ; + linkml:prefix_reference ], [ linkml:prefix_prefix "LOINC" ; linkml:prefix_reference ], - [ linkml:prefix_prefix "Xenbase" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "HANCESTRO" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "RTXKG1" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "schema" ; - linkml:prefix_reference schema: ], - [ linkml:prefix_prefix "PHAROS" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "METANETX.REACTION" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "oboformat" ; - linkml:prefix_reference OIO: ], - [ linkml:prefix_prefix "UBERGRAPH" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "SNOMEDCT" ; - linkml:prefix_reference ], + [ linkml:prefix_prefix "fabio" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "ICD10" ; + linkml:prefix_reference ], [ linkml:prefix_prefix "ScopusID" ; linkml:prefix_reference ], - [ linkml:prefix_prefix "MAXO" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "MSigDB" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "ICD0" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "KEGG.RCLASS" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "interpro" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "RXCUI" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "HsapDv" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "NCBIGene" ; - linkml:prefix_reference ], [ linkml:prefix_prefix "DGIdb" ; linkml:prefix_reference ], + [ linkml:prefix_prefix "alliancegenome" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "STY" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "XPO" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "foodb.compound" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "hetio" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "ORCID" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "schema" ; + linkml:prefix_reference schema: ], + [ linkml:prefix_prefix "GOP" ; + linkml:prefix_reference ], [ linkml:prefix_prefix "UBERON_CORE" ; linkml:prefix_reference ], - [ linkml:prefix_prefix "NBO-PROPERTY" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "INO" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "mirbase" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "KEGG.BRITE" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "KEGG.PATHWAY" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "SNPEFF" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "SNOMED" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "ICD10" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "KEGG.DGROUP" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "CLINVAR" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "CHEMBL.MECHANISM" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "FYPO" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "fabio" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "MESH" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "ChemBank" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "HCPCS" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "ExO" ; - linkml:prefix_reference ] ; + [ linkml:prefix_prefix "gff3" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "medgen" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "interpro" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "wgs" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "Xenbase" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "PHAROS" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "EDAM-TOPIC" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "PathWhiz" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "HANCESTRO" ; + linkml:prefix_reference ] ; linkml:slots , , , @@ -640,7 +640,6 @@ , , , - , , , , @@ -972,6 +971,7 @@ , , , + , , , , @@ -1157,8 +1157,8 @@ , ; linkml:source_file "biolink-model.yaml" ; - linkml:source_file_date "2021-11-08T21:37:13"^^xsd:dateTime ; - linkml:source_file_size 325053 ; + linkml:source_file_date "2021-11-08T22:02:12"^^xsd:dateTime ; + linkml:source_file_size 325059 ; linkml:subsets , , , @@ -2125,11 +2125,11 @@ linkml:domain ; linkml:domain_of ; linkml:examples [ a linkml:Example ; - skos:definition "Ehlers-Danlos syndrome, vascular type" ; - skos:example "MONDO:0017314" ], - [ a linkml:Example ; skos:definition "abnormal brain ventricle size" ; - skos:example "MP:0013229" ] ; + skos:example "MP:0013229" ], + [ a linkml:Example ; + skos:definition "Ehlers-Danlos syndrome, vascular type" ; + skos:example "MONDO:0017314" ] ; linkml:is_a ; linkml:is_usage_slot true ; linkml:local_names [ linkml:ga4gh [ skos:altLabel "annotation subject" ; @@ -2378,14 +2378,14 @@ linkml:domain ; linkml:domain_of ; linkml:examples [ a linkml:Example ; + skos:definition "abnormal circulating bilirubin level" ; + skos:example "MP:0001569" ], + [ a linkml:Example ; skos:definition "axon morphology variant" ; skos:example "WBPhenotype:0000180" ], [ a linkml:Example ; skos:definition "Hyperkinesis" ; - skos:example "HP:0002487" ], - [ a linkml:Example ; - skos:definition "abnormal circulating bilirubin level" ; - skos:example "MP:0001569" ] ; + skos:example "HP:0002487" ] ; linkml:is_a ; linkml:is_usage_slot true ; linkml:local_names [ linkml:ga4gh [ skos:altLabel "descriptor" ; @@ -4742,11 +4742,11 @@ linkml:domain ; linkml:domain_of ; linkml:examples [ a linkml:Example ; - skos:definition "chr13:g.32921033G>C (hg19) in ClinGen" ; - skos:example "ClinGen:CA024716" ], - [ a linkml:Example ; skos:definition "ClinVar representation of NM_000059.3(BRCA2):c.7007G>A (p.Arg2336His)" ; - skos:example "ClinVar:38077" ] ; + skos:example "ClinVar:38077" ], + [ a linkml:Example ; + skos:definition "chr13:g.32921033G>C (hg19) in ClinGen" ; + skos:example "ClinGen:CA024716" ] ; linkml:is_a ; linkml:is_usage_slot true ; linkml:local_names [ linkml:ga4gh [ skos:altLabel "annotation subject" ; @@ -6408,11 +6408,11 @@ linkml:domain ; linkml:domain_of ; linkml:examples [ a linkml:Example ; - skos:definition "ti282a allele from ZFIN" ; - skos:example "ZFIN:ZDB-ALT-980203-1091" ], - [ a linkml:Example ; skos:definition "NM_007294.3(BRCA1):c.2521C>T (p.Arg841Trp)" ; - skos:example "ClinVarVariant:17681" ] ; + skos:example "ClinVarVariant:17681" ], + [ a linkml:Example ; + skos:definition "ti282a allele from ZFIN" ; + skos:example "ZFIN:ZDB-ALT-980203-1091" ] ; linkml:identifier true ; linkml:is_a ; linkml:is_usage_slot true ; @@ -7436,23 +7436,6 @@ linkml:range ; linkml:slot_uri . - a linkml:SlotDefinition ; - OIO:inSubset ; - skos:definition "holds between two entities where their co-occurrence is correlated by counts of publications in which both occur, using some threshold of occurrence as defined by the edge provider." ; - skos:inScheme ; - linkml:annotations [ a linkml:Annotation ; - skos:example "True" ; - linkml:tag ] ; - linkml:definition_uri ; - linkml:domain ; - linkml:inherited true ; - linkml:is_a ; - linkml:multivalued true ; - linkml:owner ; - linkml:range ; - linkml:slot_uri ; - linkml:symmetric true . - a linkml:SlotDefinition ; OIO:inSubset ; skos:definition "holds between two entities that are observed to be located in the same place." ; @@ -8044,6 +8027,23 @@ linkml:slot_uri ; linkml:symmetric true . + a linkml:SlotDefinition ; + OIO:inSubset ; + skos:definition "holds between two entities where their co-occurrence is correlated by counts of publications in which both occur, using some threshold of occurrence as defined by the edge provider." ; + skos:inScheme ; + linkml:annotations [ a linkml:Annotation ; + skos:example "True" ; + linkml:tag ] ; + linkml:definition_uri ; + linkml:domain ; + linkml:inherited true ; + linkml:is_a ; + linkml:multivalued true ; + linkml:owner ; + linkml:range ; + linkml:slot_uri ; + linkml:symmetric true . + a linkml:SlotDefinition ; rdfs:seeAlso , ; @@ -9792,11 +9792,11 @@ linkml:inlined true ; linkml:is_a ; linkml:local_names [ a linkml:LocalName ; - skos:altLabel "activity directly negatively regulates activity of" ; - linkml:local_name_source "ro" ], - [ a linkml:LocalName ; skos:altLabel "negatively regulates" ; - linkml:local_name_source "translator" ] ; + linkml:local_name_source "translator" ], + [ a linkml:LocalName ; + skos:altLabel "activity directly negatively regulates activity of" ; + linkml:local_name_source "ro" ] ; linkml:mixins ; linkml:multivalued true ; linkml:owner ; @@ -13102,11 +13102,11 @@ linkml:domain ; linkml:domain_of ; linkml:examples [ a linkml:Example ; - skos:definition "kinase activity" ; - skos:example "GO:0016301" ], - [ a linkml:Example ; skos:definition "postsynaptic membrane" ; - skos:example "GO:0045211" ] ; + skos:example "GO:0045211" ], + [ a linkml:Example ; + skos:definition "kinase activity" ; + skos:example "GO:0016301" ] ; linkml:inlined true ; linkml:is_a ; linkml:is_usage_slot true ; @@ -18881,11 +18881,11 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t skos:inScheme ; skos:note "This class is for modeling the specific state at a locus. A single DBSNP rs ID could correspond to more than one sequence variants (e.g CIViC:1252 and CIViC:1253, two distinct BRCA2 alleles for rs28897743)" ; linkml:alt_descriptions [ a linkml:AltDescription ; - skos:definition "An entity that describes a single affected, endogenous allele. These can be of any type that matches that definition" ; - linkml:source "AGR" ], - [ a linkml:AltDescription ; skos:definition "A contiguous change at a Location" ; - linkml:source "VMC" ] ; + linkml:source "VMC" ], + [ a linkml:AltDescription ; + skos:definition "An entity that describes a single affected, endogenous allele. These can be of any type that matches that definition" ; + linkml:source "AGR" ] ; linkml:class_uri ; linkml:definition_uri ; linkml:id_prefixes "CAID", @@ -19459,11 +19459,11 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t linkml:domain_of ; linkml:is_a ; linkml:local_names [ a linkml:LocalName ; - skos:altLabel "annotation subject" ; - linkml:local_name_source "ga4gh" ], - [ a linkml:LocalName ; skos:altLabel "node with outgoing relationship" ; - linkml:local_name_source "neo4j" ] ; + linkml:local_name_source "neo4j" ], + [ a linkml:LocalName ; + skos:altLabel "annotation subject" ; + linkml:local_name_source "ga4gh" ] ; linkml:owner ; linkml:range ; linkml:required true ; diff --git a/biolink/model.py b/biolink/model.py index 5919ffdf52..69b964dd3c 100644 --- a/biolink/model.py +++ b/biolink/model.py @@ -1,5 +1,5 @@ # Auto generated from biolink-model.yaml by pythongen.py version: 0.9.0 -# Generation date: 2021-11-08T21:40:42 +# Generation date: 2021-11-08T22:05:28 # Schema: Biolink-Model # # id: https://w3id.org/biolink/biolink-model @@ -9092,8 +9092,8 @@ class slots: slots.negatively_correlated_with = Slot(uri=BIOLINK.negatively_correlated_with, name="negatively correlated with", curie=BIOLINK.curie('negatively_correlated_with'), model_uri=BIOLINK.negatively_correlated_with, domain=NamedThing, range=Optional[Union[Union[str, NamedThingId], List[Union[str, NamedThingId]]]]) -slots.co_occurs_in_literature_with = Slot(uri=BIOLINK.co_occurs_in_literature_with, name="co-occurs in literature with", curie=BIOLINK.curie('co_occurs_in_literature_with'), - model_uri=BIOLINK.co_occurs_in_literature_with, domain=NamedThing, range=Optional[Union[Union[str, NamedThingId], List[Union[str, NamedThingId]]]]) +slots.occurs_together_in_literature_with = Slot(uri=BIOLINK.occurs_together_in_literature_with, name="occurs together in literature with", curie=BIOLINK.curie('occurs_together_in_literature_with'), + model_uri=BIOLINK.occurs_together_in_literature_with, domain=NamedThing, range=Optional[Union[Union[str, NamedThingId], List[Union[str, NamedThingId]]]]) slots.coexpressed_with = Slot(uri=BIOLINK.coexpressed_with, name="coexpressed with", curie=BIOLINK.curie('coexpressed_with'), model_uri=BIOLINK.coexpressed_with, domain=None, range=Optional[Union[Union[dict, "GeneOrGeneProduct"], List[Union[dict, "GeneOrGeneProduct"]]]]) diff --git a/context.jsonld b/context.jsonld index ea6db4d509..b1cbbb8c2d 100644 --- a/context.jsonld +++ b/context.jsonld @@ -1,5 +1,5 @@ { - "_comments": "Auto generated from biolink-model.yaml by jsonldcontextgen.py version: 0.1.1\n Generation date: 2021-11-08T21:39:50\n Schema: Biolink-Model\n \n id: https://w3id.org/biolink/biolink-model\n description: Entity and association taxonomy and datamodel for life-sciences data\n license: https://creativecommons.org/publicdomain/zero/1.0/\n ", + "_comments": "Auto generated from biolink-model.yaml by jsonldcontextgen.py version: 0.1.1\n Generation date: 2021-11-08T22:04:39\n Schema: Biolink-Model\n \n id: https://w3id.org/biolink/biolink-model\n description: Entity and association taxonomy and datamodel for life-sciences data\n license: https://creativecommons.org/publicdomain/zero/1.0/\n ", "@context": { "APO": { "@id": "http://purl.obolibrary.org/obo/APO_", @@ -721,9 +721,6 @@ "close_match": { "@type": "@id" }, - "co_occurs_in_literature_with": { - "@type": "@id" - }, "coexists_with": { "@type": "@id" }, @@ -1435,6 +1432,9 @@ "occurs_in": { "@type": "@id" }, + "occurs_together_in_literature_with": { + "@type": "@id" + }, "onset_qualifier": { "@type": "@id" }, diff --git a/contextn.jsonld b/contextn.jsonld index 547c0e89ec..92bed5d888 100644 --- a/contextn.jsonld +++ b/contextn.jsonld @@ -1,5 +1,5 @@ { - "_comments": "Auto generated from biolink-model.yaml by jsonldcontextgen.py version: 0.1.1\n Generation date: 2021-11-08T21:39:56\n Schema: Biolink-Model\n \n id: https://w3id.org/biolink/biolink-model\n description: Entity and association taxonomy and datamodel for life-sciences data\n license: https://creativecommons.org/publicdomain/zero/1.0/\n ", + "_comments": "Auto generated from biolink-model.yaml by jsonldcontextgen.py version: 0.1.1\n Generation date: 2021-11-08T22:04:45\n Schema: Biolink-Model\n \n id: https://w3id.org/biolink/biolink-model\n description: Entity and association taxonomy and datamodel for life-sciences data\n license: https://creativecommons.org/publicdomain/zero/1.0/\n ", "@context": { "APO": { "@id": "http://purl.obolibrary.org/obo/APO_", @@ -721,9 +721,6 @@ "close_match": { "@type": "@id" }, - "co_occurs_in_literature_with": { - "@type": "@id" - }, "coexists_with": { "@type": "@id" }, @@ -1417,6 +1414,9 @@ "occurs_in": { "@type": "@id" }, + "occurs_together_in_literature_with": { + "@type": "@id" + }, "onset_qualifier": { "@type": "@id" },