diff --git a/biolink-model.owl.ttl b/biolink-model.owl.ttl index 6941c9a4cf..a41787ac6a 100644 --- a/biolink-model.owl.ttl +++ b/biolink-model.owl.ttl @@ -74,12 +74,12 @@ dcat:downloadURL a owl:ObjectProperty . biolink:ThingWithTaxon, biolink:VariantToEntityAssociationMixin ; dct:license "https://creativecommons.org/publicdomain/zero/1.0/" ; - pav:version "2.2.5" ; + pav:version "2.2.6" ; skos:definition "Entity and association taxonomy and datamodel for life-sciences data" ; - linkml:generation_date "2021-10-25 15:43" ; + linkml:generation_date "2021-10-25 16:00" ; linkml:metamodel_version "1.7.0" ; linkml:source_file "biolink-model.yaml" ; - linkml:source_file_date "Mon Oct 25 15:40:24 2021" ; + linkml:source_file_date "Mon Oct 25 15:58:19 2021" ; linkml:source_file_size 323656 . biolink:Activity a owl:Class ; @@ -101,13 +101,13 @@ 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:PredicateType ; - owl:onProperty rdf:predicate ; - owl:qualifiedCardinality 1 ], - [ a owl:Restriction ; owl:onClass biolink:AnatomicalEntity ; 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:AnatomicalEntity ; owl:onProperty rdf:subject ; @@ -121,20 +121,24 @@ biolink:AnatomicalEntityToAnatomicalEntityPartOfAssociation a owl:Class ; owl:onClass biolink:AnatomicalEntity ; 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:AnatomicalEntity ; owl:onProperty rdf:subject ; owl:qualifiedCardinality 1 ], + [ a owl:Restriction ; + owl:onClass biolink:PredicateType ; + owl:onProperty rdf:predicate ; + owl:qualifiedCardinality 1 ], 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" . biolink:Article a owl:Class ; rdfs:label "article" ; rdfs:subClassOf [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass linkml:String ; + owl:onProperty biolink:volume ], + [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass linkml:String ; owl:onProperty biolink:iso_abbreviation ], @@ -146,38 +150,34 @@ biolink:Article a owl:Class ; owl:maxQualifiedCardinality 1 ; owl:onClass linkml:String ; owl:onProperty biolink:issue ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty biolink:volume ], biolink:Publication . biolink:BehaviorToBehavioralFeatureAssociation a owl:Class ; rdfs:label "behavior to behavioral feature association" ; rdfs:subClassOf [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:BiologicalSex ; - owl:onProperty biolink:sex_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 ], + owl:onClass biolink:BehavioralFeature ; + owl:onProperty rdf:object ; + owl:qualifiedCardinality 1 ], [ 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 ; - owl:qualifiedCardinality 1 ], + 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:onClass biolink:Behavior ; 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:EntityToPhenotypicFeatureAssociationMixin ; skos:definition "An association between an mixture behavior and a behavioral feature manifested by the individual exhibited or has exhibited the behavior." . @@ -211,11 +211,11 @@ biolink:Book a owl:Class ; rdfs:label "book" ; rdfs:subClassOf [ a owl:Restriction ; owl:onClass linkml:String ; - owl:onProperty biolink:id ; + owl:onProperty rdf:type ; owl:qualifiedCardinality 1 ], [ a owl:Restriction ; owl:onClass linkml:String ; - owl:onProperty rdf:type ; + owl:onProperty biolink:id ; 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." . @@ -223,14 +223,6 @@ biolink:Book a owl:Class ; 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 ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:BiologicalSex ; - owl:onProperty biolink:sex_qualifier ], - [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass biolink:Onset ; owl:onProperty biolink:onset_qualifier ], @@ -238,6 +230,14 @@ biolink:CaseToPhenotypicFeatureAssociation a owl:Class ; owl:maxQualifiedCardinality 1 ; owl:onClass biolink:FrequencyValue ; owl:onProperty biolink:frequency_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:SeverityValue ; + owl:onProperty biolink:severity_qualifier ], biolink:Association, biolink:CaseToEntityAssociationMixin, biolink:EntityToPhenotypicFeatureAssociationMixin ; @@ -255,21 +255,21 @@ 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: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:CellLine ; 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 ], biolink:CellLineToDiseaseOrPhenotypicFeatureAssociation, biolink:EntityToDiseaseAssociationMixin, biolink:ModelToDiseaseAssociationMixin . @@ -277,19 +277,19 @@ 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:onClass biolink:PredicateType ; + owl:onProperty rdf:predicate ; owl:qualifiedCardinality 1 ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:MacromolecularMachineMixin ; + owl:onProperty biolink:catalyst_qualifier ], [ a owl:Restriction ; owl:onClass biolink:ChemicalEntity ; owl:onProperty rdf:subject ; 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: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: @@ -375,8 +375,8 @@ biolink:ComplexMolecularMixture a owl:Class ; biolink:ContributorAssociation a owl:Class ; rdfs:label "contributor association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:onClass biolink:Agent ; - owl:onProperty rdf:object ; + owl:onClass biolink:InformationContentEntity ; + owl:onProperty rdf:subject ; owl:qualifiedCardinality 1 ], [ a owl:Restriction ; owl:onClass biolink:PredicateType ; @@ -386,8 +386,8 @@ biolink:ContributorAssociation a owl:Class ; owl:allValuesFrom biolink:OntologyClass ; owl:onProperty biolink:qualifiers ], [ a owl:Restriction ; - owl:onClass biolink:InformationContentEntity ; - owl:onProperty rdf:subject ; + owl:onClass biolink:Agent ; + owl:onProperty rdf:object ; owl:qualifiedCardinality 1 ], biolink:Association ; skos:definition "Any association between an entity (such as a publication) and various agents that contribute to its realisation" . @@ -427,21 +427,21 @@ biolink:DiseaseToExposureEventAssociation a owl:Class ; biolink:DiseaseToPhenotypicFeatureAssociation a owl:Class ; rdfs:label "disease to phenotypic feature 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 ], + [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass biolink:FrequencyValue ; + owl:onProperty biolink:frequency_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:SeverityValue ; + owl:onProperty biolink:severity_qualifier ], biolink:Association, biolink:DiseaseToEntityAssociationMixin, biolink:EntityToPhenotypicFeatureAssociationMixin ; @@ -528,13 +528,13 @@ biolink:ExonToTranscriptRelationship a owl:Class ; biolink:ExposureEventToOutcomeAssociation a owl:Class ; rdfs:label "exposure event to outcome association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:TimeType ; - owl:onProperty biolink:has_temporal_context ], - [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass biolink:PopulationOfIndividualOrganisms ; owl:onProperty biolink:has_population_context ], + [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass biolink:TimeType ; + owl:onProperty biolink:has_temporal_context ], biolink:Association, biolink:EntityToOutcomeAssociationMixin, biolink:ExposureEventToEntityAssociationMixin ; @@ -543,13 +543,9 @@ biolink:ExposureEventToOutcomeAssociation a owl:Class ; biolink:ExposureEventToPhenotypicFeatureAssociation a owl:Class ; rdfs:label "exposure event to phenotypic feature association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:onClass biolink:ExposureEvent ; - owl:onProperty rdf:subject ; - owl:qualifiedCardinality 1 ], - [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:BiologicalSex ; - owl:onProperty biolink:sex_qualifier ], + owl:onClass biolink:FrequencyValue ; + owl:onProperty biolink:frequency_qualifier ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass biolink:Onset ; @@ -558,10 +554,14 @@ biolink:ExposureEventToPhenotypicFeatureAssociation a owl:Class ; 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:FrequencyValue ; - owl:onProperty biolink:frequency_qualifier ], + owl:onClass biolink:BiologicalSex ; + owl:onProperty biolink:sex_qualifier ], biolink:Association, biolink:EntityToPhenotypicFeatureAssociationMixin ; skos:definition "Any association between an environment and a phenotypic feature, where being in the environment influences the phenotype." . @@ -620,7 +620,7 @@ biolink:GeneRegulatoryRelationship a owl:Class ; rdfs:label "gene regulatory relationship" ; rdfs:subClassOf [ a owl:Restriction ; owl:onClass biolink:GeneOrGeneProduct ; - owl:onProperty rdf:object ; + owl:onProperty rdf:subject ; owl:qualifiedCardinality 1 ], [ a owl:Restriction ; owl:onClass biolink:PredicateType ; @@ -628,7 +628,7 @@ biolink:GeneRegulatoryRelationship a owl:Class ; owl:qualifiedCardinality 1 ], [ a owl:Restriction ; owl:onClass biolink:GeneOrGeneProduct ; - owl:onProperty rdf:subject ; + owl:onProperty rdf:object ; owl:qualifiedCardinality 1 ], biolink:Association ; skos:definition "A regulatory relationship between two genes" . @@ -637,25 +637,25 @@ biolink:GeneToExpressionSiteAssociation a owl:Class ; rdfs:label "gene to expression site association" ; rdfs:seeAlso "https://github.com/monarch-initiative/ingest-artifacts/tree/master/sources/BGee" ; rdfs:subClassOf [ a owl:Restriction ; - owl:onClass biolink:GeneOrGeneProduct ; - owl:onProperty rdf:subject ; - owl:qualifiedCardinality 1 ], - [ a owl:Restriction ; owl:onClass biolink:AnatomicalEntity ; owl:onProperty rdf:object ; owl:qualifiedCardinality 1 ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:LifeStage ; - owl:onProperty biolink:stage_qualifier ], [ a owl:Restriction ; 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:onClass biolink:PredicateType ; owl:onProperty rdf:predicate ; 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?" . @@ -663,9 +663,13 @@ 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:LifeStage ; - owl:onProperty biolink:stage_qualifier ], + owl:onClass biolink:OntologyClass ; + owl:onProperty biolink:quantifier_qualifier ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass biolink:AnatomicalEntity ; @@ -676,12 +680,8 @@ biolink:GeneToGeneCoexpressionAssociation a owl:Class ; owl:onProperty biolink:phenotypic_state ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:OntologyClass ; - owl:onProperty biolink:quantifier_qualifier ], - [ a owl:Restriction ; - owl:onClass biolink:PredicateType ; - owl:onProperty rdf:predicate ; - owl:qualifiedCardinality 1 ], + owl:onClass biolink:LifeStage ; + owl:onProperty biolink:stage_qualifier ], biolink:GeneExpressionMixin, biolink:GeneToGeneAssociation ; skos:definition "Indicates that two genes are co-expressed, generally under the same conditions." . @@ -698,6 +698,10 @@ 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:Gene ; + owl:onProperty rdf:subject ; + owl:qualifiedCardinality 1 ], + [ a owl:Restriction ; owl:onClass biolink:PredicateType ; owl:onProperty rdf:predicate ; owl:qualifiedCardinality 1 ], @@ -705,23 +709,19 @@ biolink:GeneToGeneProductRelationship a owl:Class ; owl:onClass biolink:GeneProductMixin ; owl:onProperty rdf:object ; owl:qualifiedCardinality 1 ], - [ a owl:Restriction ; - owl:onClass biolink:Gene ; - owl:onProperty rdf:subject ; - owl:qualifiedCardinality 1 ], biolink:SequenceFeatureRelationship ; skos:definition "A gene is transcribed and potentially translated to a gene product" . biolink:GeneToGoTermAssociation a owl:Class ; rdfs:label "gene to go term association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:onClass biolink:Gene ; - owl:onProperty rdf:subject ; - owl:qualifiedCardinality 1 ], - [ a owl:Restriction ; owl:onClass biolink:GeneOntologyClass ; owl:onProperty rdf:object ; owl:qualifiedCardinality 1 ], + [ a owl:Restriction ; + owl:onClass biolink:Gene ; + owl:onProperty rdf:subject ; + owl:qualifiedCardinality 1 ], biolink:FunctionalAssociation ; skos:altLabel "functional association" ; skos:exactMatch WBVocab:Gene-GO-Association . @@ -732,22 +732,22 @@ biolink:GeneToPhenotypicFeatureAssociation a owl:Class ; 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: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:onClass biolink:GeneOrGeneProduct ; owl:onProperty rdf:subject ; owl:qualifiedCardinality 1 ], + [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass biolink:SeverityValue ; + owl:onProperty biolink:severity_qualifier ], biolink:Association, biolink:EntityToPhenotypicFeatureAssociationMixin, biolink:GeneToEntityAssociationMixin ; @@ -774,12 +774,12 @@ biolink:Genome a owl:Class ; biolink:GenomicBackgroundExposure a owl:Class ; rdfs:label "genomic background exposure" ; rdfs:subClassOf [ a owl:Restriction ; + owl:allValuesFrom biolink:Gene ; + owl:onProperty biolink:has_gene_or_gene_product ], + [ 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:allValuesFrom biolink:OrganismTaxon ; owl:onProperty biolink:in_taxon ], @@ -807,10 +807,6 @@ biolink:GenotypeAsAModelOfDiseaseAssociation a owl:Class ; biolink:GenotypeToGeneAssociation a owl:Class ; rdfs:label "genotype to gene association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:onClass biolink:PredicateType ; - owl:onProperty rdf:predicate ; - owl:qualifiedCardinality 1 ], - [ a owl:Restriction ; owl:onClass biolink:Genotype ; owl:onProperty rdf:subject ; owl:qualifiedCardinality 1 ], @@ -818,6 +814,10 @@ biolink:GenotypeToGeneAssociation a owl:Class ; 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 ], 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" . @@ -844,14 +844,6 @@ biolink:GenotypeToPhenotypicFeatureAssociation a owl:Class ; owl:onClass biolink:Genotype ; 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:onClass biolink:PredicateType ; - owl:onProperty rdf:predicate ; - owl:qualifiedCardinality 1 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass biolink:FrequencyValue ; @@ -860,6 +852,14 @@ biolink:GenotypeToPhenotypicFeatureAssociation 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:onClass biolink:PredicateType ; + owl:onProperty rdf:predicate ; + owl:qualifiedCardinality 1 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass biolink:SeverityValue ; @@ -875,14 +875,14 @@ biolink:GenotypeToVariantAssociation a owl:Class ; owl:onClass biolink:Genotype ; owl:onProperty rdf:subject ; owl:qualifiedCardinality 1 ], - [ a owl:Restriction ; - owl:onClass biolink:SequenceVariant ; - 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:SequenceVariant ; + owl:onProperty rdf:object ; + owl:qualifiedCardinality 1 ], biolink:Association ; skos:definition "Any association between a genotype and a sequence variant." . @@ -1004,14 +1004,14 @@ biolink:MaterialSampleDerivationAssociation a owl:Class ; 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:NamedThing ; owl:onProperty rdf:object ; 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 material sample and the material entity from which it is derived." . @@ -1063,6 +1063,10 @@ biolink:MortalityOutcome a owl:Class ; biolink:NamedThingToInformationContentEntityAssociation a owl:Class ; rdfs:label "named thing to information content entity 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 ], @@ -1070,23 +1074,19 @@ biolink:NamedThingToInformationContentEntityAssociation a owl:Class ; owl:onClass biolink:Publication ; owl:onProperty rdf:object ; owl:qualifiedCardinality 1 ], - [ a owl:Restriction ; - owl:onClass biolink:PredicateType ; - owl:onProperty rdf:predicate ; - 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)." . 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 ; + rdfs:subClassOf [ 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:NamedThing ; owl:onProperty rdf:object ; @@ -1097,20 +1097,20 @@ biolink:OrganismTaxonToEnvironmentAssociation a owl:Class ; biolink:OrganismTaxonToOrganismTaxonInteraction a owl:Class ; rdfs:label "organism taxon to organism taxon interaction" ; rdfs:subClassOf [ 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:associated_environmental_context ], [ 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:onProperty rdf:object ; owl:qualifiedCardinality 1 ], [ a owl:Restriction ; owl:onClass biolink:OrganismTaxon ; - owl:onProperty rdf:object ; + owl:onProperty rdf:subject ; owl:qualifiedCardinality 1 ], 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" . @@ -1118,10 +1118,6 @@ biolink:OrganismTaxonToOrganismTaxonInteraction a owl:Class ; biolink:OrganismTaxonToOrganismTaxonSpecialization a owl:Class ; rdfs:label "organism taxon to organism taxon specialization" ; rdfs:subClassOf [ a owl:Restriction ; - owl:onClass biolink:OrganismTaxon ; - owl:onProperty rdf:subject ; - owl:qualifiedCardinality 1 ], - [ a owl:Restriction ; owl:onClass biolink:OrganismTaxon ; owl:onProperty rdf:object ; owl:qualifiedCardinality 1 ], @@ -1129,12 +1125,20 @@ biolink:OrganismTaxonToOrganismTaxonSpecialization a owl:Class ; 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 ], biolink:OrganismTaxonToOrganismTaxonAssociation ; skos:definition "A child-parent relationship between two taxa. For example: Homo sapiens subclass_of Homo" . biolink:OrganismToOrganismAssociation a owl:Class ; rdfs:label "organism to organism association" ; rdfs:subClassOf [ a owl:Restriction ; + owl:onClass biolink:IndividualOrganism ; + owl:onProperty rdf:object ; + owl:qualifiedCardinality 1 ], + [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass linkml:String ; owl:onProperty biolink:relation ], @@ -1142,18 +1146,14 @@ biolink:OrganismToOrganismAssociation a owl:Class ; owl:onClass biolink:IndividualOrganism ; owl:onProperty rdf:subject ; owl:qualifiedCardinality 1 ], - [ a owl:Restriction ; - owl:onClass biolink:IndividualOrganism ; - owl:onProperty rdf:object ; - 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 ], + owl:onClass biolink:Onset ; + owl:onProperty biolink:onset_qualifier ], [ a owl:Restriction ; owl:onClass biolink:OrganismalEntity ; owl:onProperty rdf:subject ; @@ -1164,8 +1164,8 @@ biolink:OrganismalEntityAsAModelOfDiseaseAssociation a owl:Class ; owl:onProperty biolink:severity_qualifier ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:Onset ; - owl:onProperty biolink:onset_qualifier ], + owl:onClass biolink:FrequencyValue ; + owl:onProperty biolink:frequency_qualifier ], biolink:Association, biolink:EntityToDiseaseAssociationMixin, biolink:ModelToDiseaseAssociationMixin . @@ -1173,17 +1173,13 @@ biolink:OrganismalEntityAsAModelOfDiseaseAssociation a owl:Class ; biolink:PairwiseMolecularInteraction a owl:Class ; rdfs:label "pairwise molecular interaction" ; rdfs:subClassOf [ a owl:Restriction ; - owl:onClass biolink:MolecularEntity ; - owl:onProperty rdf:subject ; - owl:qualifiedCardinality 1 ], - [ a owl:Restriction ; - owl:onClass linkml:String ; - owl:onProperty biolink:id ; - owl:qualifiedCardinality 1 ], - [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass biolink:OntologyClass ; owl:onProperty biolink:interacting_molecules_category ], + [ a owl:Restriction ; + owl:onClass biolink:MolecularEntity ; + owl:onProperty rdf:object ; + owl:qualifiedCardinality 1 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass linkml:String ; @@ -1194,7 +1190,11 @@ biolink:PairwiseMolecularInteraction a owl:Class ; owl:qualifiedCardinality 1 ], [ a owl:Restriction ; owl:onClass biolink:MolecularEntity ; - owl:onProperty rdf:object ; + owl:onProperty rdf:subject ; + owl:qualifiedCardinality 1 ], + [ a owl:Restriction ; + owl:onClass linkml:String ; + owl:onProperty biolink:id ; owl:qualifiedCardinality 1 ], biolink:PairwiseGeneToGeneInteraction ; skos:definition "An interaction at the molecular level between two physical entities" . @@ -1294,6 +1294,10 @@ biolink:PhysiologicalProcess a owl:Class ; biolink:PopulationToPopulationAssociation a owl:Class ; rdfs:label "population to population association" ; rdfs:subClassOf [ a owl:Restriction ; + owl:onClass biolink:PopulationOfIndividualOrganisms ; + owl:onProperty rdf:subject ; + owl:qualifiedCardinality 1 ], + [ a owl:Restriction ; owl:onClass biolink:PredicateType ; owl:onProperty rdf:predicate ; owl:qualifiedCardinality 1 ], @@ -1301,10 +1305,6 @@ biolink:PopulationToPopulationAssociation a owl:Class ; owl:onClass biolink:PopulationOfIndividualOrganisms ; owl:onProperty rdf:object ; owl:qualifiedCardinality 1 ], - [ a owl:Restriction ; - owl:onClass biolink:PopulationOfIndividualOrganisms ; - owl:onProperty rdf:subject ; - owl:qualifiedCardinality 1 ], biolink:Association ; skos:definition "An association between a two populations" . @@ -1342,12 +1342,12 @@ 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, @@ -1369,13 +1369,13 @@ biolink:SensitivityQuantifier a owl:Class ; biolink:SequenceVariantModulatesTreatmentAssociation a owl:Class ; rdfs:label "sequence variant modulates treatment association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:onClass biolink:Treatment ; - owl:onProperty rdf:object ; - owl:qualifiedCardinality 1 ], - [ a owl:Restriction ; owl:onClass biolink:SequenceVariant ; owl:onProperty rdf:subject ; owl:qualifiedCardinality 1 ], + [ a owl:Restriction ; + owl:onClass biolink:Treatment ; + owl:onProperty rdf:object ; + owl:qualifiedCardinality 1 ], 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:note "An alternate way to model the same information could be via a qualifier" . @@ -1383,9 +1383,9 @@ 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:id ; - owl:qualifiedCardinality 1 ], + owl:onProperty biolink:volume ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass linkml:String ; @@ -1395,13 +1395,13 @@ biolink:Serial a owl:Class ; owl:onProperty rdf:type ; owl:qualifiedCardinality 1 ], [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; owl:onClass linkml:String ; - owl:onProperty biolink:issue ], + owl:onProperty biolink:id ; + owl:qualifiedCardinality 1 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass linkml:String ; - owl:onProperty biolink:volume ], + owl:onProperty biolink:issue ], 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." . @@ -1437,16 +1437,16 @@ biolink:Snv a owl:Class ; biolink:SocioeconomicExposure a owl:Class ; rdfs:label "socioeconomic exposure" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:TimeType ; - owl:onProperty biolink:timepoint ], - [ a owl:Class ; + rdfs:subClassOf [ a owl:Class ; owl:intersectionOf ( [ a owl:Restriction ; owl:allValuesFrom biolink:SocioeconomicAttribute ; owl:onProperty biolink:has_attribute ] [ a owl:Restriction ; owl:onProperty biolink:has_attribute ; owl:someValuesFrom biolink:SocioeconomicAttribute ] ) ], + [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass biolink:TimeType ; + owl:onProperty biolink:timepoint ], biolink:ExposureEvent ; skos:definition "A socioeconomic exposure is a factor relating to social and financial status of an affected individual (e.g. poverty)." . @@ -1463,11 +1463,11 @@ biolink:TaxonToTaxonAssociation a owl:Class ; owl:onProperty biolink:relation ], [ a owl:Restriction ; owl:onClass biolink:OrganismTaxon ; - owl:onProperty rdf:object ; + owl:onProperty rdf:subject ; owl:qualifiedCardinality 1 ], [ a owl:Restriction ; owl:onClass biolink:OrganismTaxon ; - owl:onProperty rdf:subject ; + owl:onProperty rdf:object ; owl:qualifiedCardinality 1 ], biolink:Association . @@ -1503,25 +1503,25 @@ 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: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 ], + 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:LifeStage ; - owl:onProperty biolink:stage_qualifier ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:OntologyClass ; - owl:onProperty biolink:quantifier_qualifier ], + 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)" . @@ -1529,25 +1529,25 @@ biolink:VariantToGeneExpressionAssociation a owl:Class ; biolink:VariantToPhenotypicFeatureAssociation a owl:Class ; rdfs:label "variant to phenotypic feature association" ; rdfs:subClassOf [ a owl:Restriction ; + owl:onClass biolink:SequenceVariant ; + owl:onProperty rdf:subject ; + owl:qualifiedCardinality 1 ], + [ 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: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:SequenceVariant ; - owl:onProperty rdf:subject ; - owl:qualifiedCardinality 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 ], + owl:onClass biolink:SeverityValue ; + owl:onProperty biolink:severity_qualifier ], biolink:Association, biolink:EntityToPhenotypicFeatureAssociationMixin, biolink:VariantToEntityAssociationMixin . @@ -1558,10 +1558,6 @@ biolink:VariantToPopulationAssociation a owl:Class ; owl:maxQualifiedCardinality 1 ; owl:onClass linkml:Double ; owl:onProperty biolink:has_percentage ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:Integer ; - owl:onProperty biolink:has_total ], [ a owl:Restriction ; owl:onClass biolink:SequenceVariant ; owl:onProperty rdf:subject ; @@ -1574,14 +1570,18 @@ biolink:VariantToPopulationAssociation a owl:Class ; owl:maxQualifiedCardinality 1 ; owl:onClass linkml:Integer ; 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 biolink:FrequencyValue ; owl:onProperty biolink:frequency_qualifier ], [ a owl:Restriction ; - owl:onClass biolink:PopulationOfIndividualOrganisms ; - owl:onProperty rdf:object ; - owl:qualifiedCardinality 1 ], + owl:maxQualifiedCardinality 1 ; + owl:onClass linkml:Integer ; + owl:onProperty biolink:has_total ], biolink:Association, biolink:FrequencyQualifierMixin, biolink:FrequencyQuantifier, @@ -2096,11 +2096,11 @@ biolink:BookChapter a owl:Class ; rdfs:subClassOf [ 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 ; @@ -2223,13 +2223,13 @@ 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:Double ; + owl:onProperty biolink:has_quotient ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass linkml:Integer ; @@ -2244,17 +2244,13 @@ biolink:FrequencyQuantifier a owl:Class ; biolink:GenotypeToDiseaseAssociation a owl:Class ; rdfs:label "genotype to disease association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:onClass biolink:NamedThing ; - owl:onProperty rdf:object ; - owl:qualifiedCardinality 1 ], + owl:maxQualifiedCardinality 1 ; + owl:onClass biolink:SeverityValue ; + owl:onProperty biolink:severity_qualifier ], [ a owl:Restriction ; owl:onClass biolink:PredicateType ; owl:onProperty rdf:predicate ; 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 ; @@ -2263,6 +2259,10 @@ biolink:GenotypeToDiseaseAssociation a owl:Class ; 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:maxQualifiedCardinality 1 ; owl:onClass biolink:FrequencyValue ; @@ -2300,13 +2300,13 @@ 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)" . @@ -2385,6 +2385,9 @@ biolink:Treatment a owl:Class ; rdfs:subClassOf [ a owl:Restriction ; owl:allValuesFrom biolink:Drug ; owl:onProperty biolink:has_drug ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:Device ; + owl:onProperty biolink:has_device ], [ a owl:Restriction ; owl:allValuesFrom biolink:Procedure ; owl:onProperty biolink:has_procedure ], @@ -2392,9 +2395,6 @@ biolink:Treatment a owl:Class ; owl:maxQualifiedCardinality 1 ; owl:onClass biolink:TimeType ; owl:onProperty biolink:timepoint ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:Device ; - owl:onProperty biolink:has_device ], biolink:ChemicalOrDrugOrTreatment, biolink:ExposureEvent, biolink:NamedThing ; @@ -2408,28 +2408,28 @@ biolink:Treatment a owl:Class ; biolink:VariantToDiseaseAssociation a owl:Class ; rdfs:label "variant to 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:Onset ; owl:onProperty biolink:onset_qualifier ], + [ 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:onProperty rdf:object ; 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: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:onProperty rdf:subject ; owl:qualifiedCardinality 1 ], biolink:Association, biolink:EntityToDiseaseAssociationMixin, @@ -4196,11 +4196,11 @@ 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 . @@ -4284,13 +4284,13 @@ biolink:EntityToExposureEventAssociationMixin a owl:Class ; biolink:EntityToFeatureOrDiseaseQualifiersMixin a owl:Class ; rdfs:label "entity to feature or disease qualifiers mixin" ; 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:Onset ; owl:onProperty biolink:onset_qualifier ], + [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass biolink:SeverityValue ; + owl:onProperty biolink:severity_qualifier ], biolink:FrequencyQualifierMixin, linkml:mixin ; skos:definition "Qualifiers for entity to disease or phenotype associations." . @@ -4339,6 +4339,10 @@ biolink:GeneToDiseaseAssociation a owl:Class ; 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 ; @@ -4347,10 +4351,6 @@ biolink:GeneToDiseaseAssociation a owl:Class ; owl:maxQualifiedCardinality 1 ; owl:onClass biolink:SeverityValue ; owl:onProperty biolink:severity_qualifier ], - [ a owl:Restriction ; - owl:onClass biolink:GeneOrGeneProduct ; - owl:onProperty rdf:subject ; - owl:qualifiedCardinality 1 ], biolink:Association, biolink:EntityToDiseaseAssociationMixin, biolink:GeneToEntityAssociationMixin ; @@ -4688,11 +4688,11 @@ biolink:DatasetSummary a owl:Class ; rdfs:subClassOf [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass linkml:String ; - owl:onProperty schema:logo ], + owl:onProperty biolink:source_web_page ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass linkml:String ; - owl:onProperty biolink:source_web_page ], + owl:onProperty schema:logo ], biolink:InformationContentEntity ; skos:definition "an item that holds summary level information about a dataset." . @@ -4707,30 +4707,30 @@ biolink:DiseaseToEntityAssociationMixin a owl:Class ; biolink:Entity a owl:Class ; rdfs:label "entity" ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom biolink:Agent ; - owl:onProperty biolink:provided_by ], - [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; + owl:onClass biolink:LabelType ; + owl:onProperty biolink:source ], + [ a owl:Restriction ; owl:onClass linkml:String ; - owl:onProperty rdf:type ], + owl:onProperty biolink:id ; + owl:qualifiedCardinality 1 ], [ a owl:Restriction ; owl:allValuesFrom biolink:Attribute ; owl:onProperty biolink:has_attribute ], [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; owl:onClass linkml:String ; - owl:onProperty biolink:id ; - owl:qualifiedCardinality 1 ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:CategoryType ; - owl:onProperty biolink:category ], + owl:onProperty rdf:type ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass biolink:NarrativeText ; owl:onProperty dct:description ], [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:LabelType ; - owl:onProperty biolink:source ], + 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:IriType ; @@ -4754,20 +4754,20 @@ biolink:GeneExpressionMixin a owl:Class ; rdfs:label "gene expression mixin" ; rdfs:subClassOf [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:LifeStage ; - owl:onProperty biolink:stage_qualifier ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:DiseaseOrPhenotypicFeature ; - owl:onProperty biolink:phenotypic_state ], + owl:onClass biolink:OntologyClass ; + owl:onProperty biolink:quantifier_qualifier ], [ 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 ; - owl:onProperty biolink:quantifier_qualifier ], + owl:onClass biolink:DiseaseOrPhenotypicFeature ; + owl:onProperty biolink:phenotypic_state ], + [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass biolink:LifeStage ; + owl:onProperty biolink:stage_qualifier ], linkml:mixin ; skos:definition "Observed gene expression intensity, context (site, stage) and associated phenotypic status within which the expression occurs." . @@ -4845,11 +4845,11 @@ biolink:PlanetaryEntity a owl:Class ; biolink:Protein a owl:Class ; rdfs:label "protein" ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom biolink:LabelType ; - owl:onProperty biolink:synonym ], - [ a owl:Restriction ; owl:allValuesFrom linkml:Uriorcurie ; owl:onProperty biolink:xref ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:LabelType ; + owl:onProperty biolink:synonym ], biolink:GeneProductMixin, biolink:Polypeptide, biolink:ThingWithTaxon ; @@ -5255,16 +5255,16 @@ biolink:DatasetVersion a owl:Class ; rdfs:label "dataset version" ; rdfs:subClassOf [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:Dataset ; - owl:onProperty dct:source ], + owl:onClass linkml:String ; + owl:onProperty pav:version ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass biolink:DatasetDistribution ; owl:onProperty dct:distribution ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty pav:version ], + owl:onClass biolink:Dataset ; + owl:onProperty dct:source ], biolink:InformationContentEntity ; skos:definition "an item that holds version level information about a dataset." . @@ -5349,13 +5349,13 @@ biolink:PathologicalEntityMixin a owl:Class ; biolink:QuantityValue a owl:Class ; rdfs:label "quantity value" ; rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:Double ; - owl:onProperty biolink:has_numeric_value ], - [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass biolink:Unit ; owl:onProperty biolink:has_unit ], + [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass linkml:Double ; + owl:onProperty biolink:has_numeric_value ], 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" . @@ -5515,11 +5515,11 @@ biolink:ChemicalMixture a owl:Class ; rdfs:subClassOf [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass linkml:String ; - owl:onProperty biolink:drug_regulatory_status_world_wide ], + owl:onProperty biolink:highest_FDA_approval_status ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass linkml:String ; - owl:onProperty biolink:highest_FDA_approval_status ], + owl:onProperty biolink:drug_regulatory_status_world_wide ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass biolink:ChemicalMixture ; @@ -5530,11 +5530,11 @@ biolink:ChemicalMixture a owl:Class ; biolink:GeneProductMixin a owl:Class ; rdfs:label "gene product mixin" ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom biolink:LabelType ; - owl:onProperty biolink:synonym ], - [ a owl:Restriction ; owl:allValuesFrom linkml:Uriorcurie ; owl:onProperty biolink:xref ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:LabelType ; + owl:onProperty biolink:synonym ], biolink:GeneOrGeneProduct, linkml:mixin ; skos:definition "The functional molecular product of a single gene locus. Gene products are either proteins or functional RNA molecules." ; @@ -5595,13 +5595,13 @@ biolink:correlated_with 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 ], + [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass biolink:NarrativeText ; + owl:onProperty dct:description ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass biolink:BiologicalSex ; @@ -5612,16 +5612,16 @@ biolink:EntityToPhenotypicFeatureAssociationMixin a owl:Class ; biolink:Genotype a owl:Class ; rdfs:label "genotype" ; rdfs:subClassOf [ 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 ], [ 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 ], biolink:BiologicalEntity, biolink:GenomicEntity, biolink:OntologyClass, @@ -5679,12 +5679,12 @@ biolink:MolecularActivity a owl:Class ; rdfs:subClassOf [ a owl:Restriction ; owl:allValuesFrom biolink:MolecularEntity ; owl:onProperty biolink:has_output ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:MolecularEntity ; - owl:onProperty biolink:has_input ], [ a owl:Restriction ; owl:allValuesFrom biolink:MacromolecularMachineMixin ; owl:onProperty biolink:enabled_by ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:MolecularEntity ; + owl:onProperty biolink:has_input ], biolink:BiologicalProcessOrActivity, biolink:Occurrent, biolink:OntologyClass ; @@ -5722,16 +5722,16 @@ biolink:sex_qualifier a owl:ObjectProperty ; biolink:Agent a owl:Class ; rdfs:label "agent" ; rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:LabelType ; - owl:onProperty rdfs:label ], + owl:allValuesFrom linkml:Uriorcurie ; + owl:onProperty biolink:affiliation ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass linkml:String ; owl:onProperty biolink:address ], [ a owl:Restriction ; - owl:allValuesFrom linkml:Uriorcurie ; - owl:onProperty biolink:affiliation ], + owl:maxQualifiedCardinality 1 ; + owl:onClass biolink:LabelType ; + owl:onProperty rdfs:label ], [ a owl:Restriction ; owl:onClass linkml:String ; owl:onProperty biolink:id ; @@ -5751,14 +5751,14 @@ biolink:Agent a owl:Class ; biolink:BiologicalProcessOrActivity a owl:Class ; rdfs:label "biological process or activity" ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom biolink:PhysicalEntity ; - owl:onProperty biolink:enabled_by ], + owl:allValuesFrom biolink:BiologicalProcessOrActivity ; + owl:onProperty biolink:has_output ], [ a owl:Restriction ; owl:allValuesFrom biolink:BiologicalProcessOrActivity ; owl:onProperty biolink:has_input ], [ a owl:Restriction ; - owl:allValuesFrom biolink:BiologicalProcessOrActivity ; - owl:onProperty biolink:has_output ], + owl:allValuesFrom biolink:PhysicalEntity ; + owl:onProperty biolink:enabled_by ], biolink:BiologicalEntity, biolink:Occurrent, biolink:OntologyClass ; @@ -5771,6 +5771,10 @@ biolink:BiologicalSequence a owl:Class ; biolink:GenomicSequenceLocalization a owl:Class ; rdfs:label "genomic sequence localization" ; rdfs:subClassOf [ a owl:Restriction ; + owl:onClass biolink:PredicateType ; + owl:onProperty rdf:predicate ; + owl:qualifiedCardinality 1 ], + [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass linkml:Integer ; owl:onProperty biolink:start_interbase_coordinate ], @@ -5778,14 +5782,14 @@ biolink:GenomicSequenceLocalization a owl:Class ; owl:onClass biolink:NucleicAcidEntity ; owl:onProperty rdf:subject ; owl:qualifiedCardinality 1 ], - [ a owl:Restriction ; - owl:onClass biolink:NucleicAcidEntity ; - owl:onProperty rdf:object ; - owl:qualifiedCardinality 1 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass ; owl:onProperty biolink:genome_build ], + [ a owl:Restriction ; + owl:onClass biolink:NucleicAcidEntity ; + owl:onProperty rdf:object ; + owl:qualifiedCardinality 1 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass linkml:Integer ; @@ -5794,10 +5798,6 @@ biolink:GenomicSequenceLocalization a owl:Class ; owl:maxQualifiedCardinality 1 ; owl:onClass ; owl:onProperty biolink:strand ], - [ a owl:Restriction ; - owl:onClass biolink:PredicateType ; - owl:onProperty rdf:predicate ; - owl:qualifiedCardinality 1 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass ; @@ -5810,10 +5810,6 @@ 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:IriType ; - owl:onProperty biolink:iri ], - [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass biolink:LabelType ; owl:onProperty biolink:source ], @@ -5821,6 +5817,14 @@ biolink:Attribute a owl:Class ; owl:maxQualifiedCardinality 1 ; owl:onClass biolink:LabelType ; owl:onProperty rdfs:label ], + [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass biolink:IriType ; + owl:onProperty biolink:iri ], + [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass biolink:NamedThing ; + owl:onProperty biolink:has_qualitative_value ], [ a owl:Restriction ; owl:onClass biolink:OntologyClass ; owl:onProperty biolink:has_attribute_type ; @@ -5828,10 +5832,6 @@ biolink:Attribute a owl:Class ; [ a owl:Restriction ; owl:allValuesFrom biolink:QuantityValue ; owl:onProperty biolink:has_quantitative_value ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:NamedThing ; - owl:onProperty biolink:has_qualitative_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." ; @@ -5913,14 +5913,14 @@ biolink:InformationContentEntity a owl:Class ; owl:maxQualifiedCardinality 1 ; owl:onClass linkml:String ; owl:onProperty biolink:format ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:Date ; - owl:onProperty biolink:creation_date ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass linkml:String ; owl:onProperty biolink:rights ], + [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass linkml:Date ; + owl:onProperty biolink:creation_date ], biolink:NamedThing ; skos:altLabel "information", "information artefact", @@ -5987,32 +5987,32 @@ biolink:TimeType a owl:Class ; biolink:Publication a owl:Class ; rdfs:label "publication" ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom linkml:Uriorcurie ; - owl:onProperty biolink:xref ], - [ 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:maxQualifiedCardinality 1 ; - owl:onClass biolink:LabelType ; - owl:onProperty rdfs:label ], - [ a owl:Restriction ; - owl:allValuesFrom linkml:String ; - owl:onProperty biolink:pages ], [ a owl:Restriction ; owl:allValuesFrom linkml:Uriorcurie ; owl:onProperty biolink:mesh_terms ], [ a owl:Restriction ; - owl:allValuesFrom linkml:String ; - owl:onProperty biolink:authors ], + owl:allValuesFrom linkml:Uriorcurie ; + owl:onProperty biolink:xref ], [ a owl:Restriction ; owl:onClass linkml:String ; owl:onProperty biolink:id ; owl:qualifiedCardinality 1 ], + [ a owl:Restriction ; + owl:allValuesFrom linkml:String ; + owl:onProperty biolink:keywords ], + [ a owl:Restriction ; + owl:allValuesFrom linkml:String ; + owl:onProperty biolink:authors ], + [ a owl:Restriction ; + owl:allValuesFrom linkml:String ; + owl:onProperty biolink:pages ], + [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass biolink:LabelType ; + owl:onProperty rdfs:label ], [ a owl:Restriction ; owl:onClass linkml:String ; owl:onProperty dct:type ; @@ -6112,19 +6112,19 @@ biolink:DiseaseOrPhenotypicFeature a owl:Class ; biolink:SequenceVariant a owl:Class ; rdfs:label "sequence variant" ; rdfs:subClassOf [ a owl:Restriction ; - owl:onClass linkml:String ; - owl:onProperty biolink:id ; - owl:qualifiedCardinality 1 ], - [ a owl:Restriction ; owl:allValuesFrom biolink:OrganismTaxon ; owl:onProperty biolink:in_taxon ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:Gene ; - owl:onProperty biolink:has_gene ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass biolink:BiologicalSequence ; owl:onProperty biolink:has_biological_sequence ], + [ a owl:Restriction ; + owl:onClass linkml:String ; + owl:onProperty biolink:id ; + owl:qualifiedCardinality 1 ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:Gene ; + owl:onProperty biolink:has_gene ], biolink:BiologicalEntity, biolink:GenomicEntity, biolink:OntologyClass, @@ -6142,20 +6142,20 @@ 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:maxQualifiedCardinality 1 ; owl:onClass biolink:ChemicalEntity ; owl:onProperty biolink:trade_name ], + [ 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:allValuesFrom ; - owl:onProperty biolink:available_from ], biolink:ChemicalEntityOrGeneOrGeneProduct, biolink:ChemicalEntityOrProteinOrPolypeptide, biolink:ChemicalOrDrugOrTreatment, @@ -6184,12 +6184,12 @@ rdf:predicate a owl:ObjectProperty . biolink:OrganismTaxon a owl:Class ; rdfs:label "organism taxon" ; rdfs:subClassOf [ a owl:Restriction ; + owl:allValuesFrom biolink:OrganismTaxon ; + owl:onProperty biolink:subclass_of ], + [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass biolink:TaxonomicRank ; owl:onProperty biolink:has_taxonomic_rank ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:OrganismTaxon ; - owl:onProperty biolink:subclass_of ], biolink:NamedThing ; skos:altLabel "taxon", "taxonomic classification" ; @@ -6211,12 +6211,12 @@ biolink:association_slot a owl:ObjectProperty ; biolink:NucleicAcidEntity a owl:Class ; rdfs:label "nucleic acid entity" ; 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:GenomicEntity, biolink:MolecularEntity, biolink:OntologyClass, @@ -6231,22 +6231,22 @@ biolink:NucleicAcidEntity a owl:Class ; biolink:Gene a owl:Class ; rdfs:label "gene" ; rdfs:subClassOf [ 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 ], [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:BiologicalSequence ; - owl:onProperty biolink:has_biological_sequence ], + owl:allValuesFrom linkml:Uriorcurie ; + owl:onProperty biolink:xref ], [ a owl:Restriction ; owl:allValuesFrom biolink:OrganismTaxon ; owl:onProperty biolink:in_taxon ], [ a owl:Restriction ; - owl:allValuesFrom linkml:Uriorcurie ; - owl:onProperty biolink:xref ], + owl:maxQualifiedCardinality 1 ; + owl:onClass biolink:BiologicalSequence ; + owl:onProperty biolink:has_biological_sequence ], + [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass linkml:String ; + owl:onProperty biolink:symbol ], biolink:BiologicalEntity, biolink:ChemicalEntityOrGeneOrGeneProduct, biolink:GeneOrGeneProduct, @@ -6304,41 +6304,41 @@ 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: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:Boolean ; + owl:onProperty biolink:negated ], [ a owl:Restriction ; owl:allValuesFrom biolink:EvidenceType ; owl:onProperty biolink:has_evidence ], [ a owl:Restriction ; - owl:allValuesFrom biolink:OntologyClass ; - owl:onProperty biolink:qualifiers ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:Publication ; - owl:onProperty biolink:publications ], + owl:maxQualifiedCardinality 1 ; + owl:onClass linkml:String ; + owl:onProperty rdf:type ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass linkml:String ; owl:onProperty biolink:relation ], [ a owl:Restriction ; - owl:onClass biolink:NamedThing ; - owl:onProperty rdf:object ; + owl:onClass biolink:PredicateType ; + owl:onProperty rdf:predicate ; 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:maxQualifiedCardinality 1 ; - owl:onClass linkml:Boolean ; - owl:onProperty biolink:negated ], + owl:allValuesFrom biolink:OntologyClass ; + owl:onProperty biolink:qualifiers ], [ 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:NamedThing ; + owl:onProperty rdf:subject ; + owl:qualifiedCardinality 1 ], biolink:Entity ; skos:definition "A typed association between two entities, supported by evidence" ; skos:exactMatch OBAN:association, diff --git a/biolink-model.ttl b/biolink-model.ttl index 199481d6fd..620c342f8e 100644 --- a/biolink-model.ttl +++ b/biolink-model.ttl @@ -13,7 +13,7 @@ a linkml:SchemaDefinition ; dcterms:license "https://creativecommons.org/publicdomain/zero/1.0/" ; - pav:version "2.2.5" ; + pav:version "2.2.6" ; skos:definition "Entity and association taxonomy and datamodel for life-sciences data" ; linkml:classes , , @@ -296,232 +296,232 @@ , , ; - linkml:generation_date "2021-10-25 15:43"^^xsd:dateTime ; + linkml:generation_date "2021-10-25 16:01"^^xsd:dateTime ; linkml:id ; linkml:imports linkml:types ; linkml:metamodel_version "1.7.0" ; - linkml:prefixes [ linkml:prefix_prefix "RXCUI" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "WBVocab" ; - linkml:prefix_reference ], + linkml:prefixes [ linkml:prefix_prefix "COG" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "CID" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "UBERGRAPH" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "HANCESTRO" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "KEGG.ENZYME" ; + linkml:prefix_reference ], [ linkml:prefix_prefix "ICD9" ; linkml:prefix_reference ], + [ linkml:prefix_prefix "MSigDB" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "gtpo" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "gff3" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "EDAM-FORMAT" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "VANDF" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "INO" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "schema" ; + linkml:prefix_reference schema: ], + [ linkml:prefix_prefix "dct" ; + linkml:prefix_reference dcterms: ], + [ linkml:prefix_prefix "CHADO" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "wgs" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "LOINC" ; + linkml:prefix_reference ], [ linkml:prefix_prefix "VMC" ; linkml:prefix_reference ], - [ linkml:prefix_prefix "KEGG.PATHWAY" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "PHAROS" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "isni" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "UBERON_CORE" ; - linkml:prefix_reference ], + [ linkml:prefix_prefix "ChemBank" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "Aeolus" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "FYPO" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "RTXKG1" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "GAMMA" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "KEGG.DGROUP" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "chembio" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "RO" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "os" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "MESH" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "PathWhiz" ; + linkml:prefix_reference ], [ linkml:prefix_prefix "medgen" ; linkml:prefix_reference ], - [ linkml:prefix_prefix "STY" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "KEGG.BRITE" ; - linkml:prefix_reference ], + [ linkml:prefix_prefix "prov" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "RXNORM" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "UBERON_CORE" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "ICD0" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "ICD10" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "CTD" ; + linkml:prefix_reference ], [ linkml:prefix_prefix "COAR_RESOURCE" ; linkml:prefix_reference ], - [ linkml:prefix_prefix "UBERGRAPH" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "GOREL" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "CHADO" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "REPODB" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "foodb.compound" ; - linkml:prefix_reference ], + [ linkml:prefix_prefix "isni" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "GSID" ; + linkml:prefix_reference ], [ linkml:prefix_prefix "apollo" ; linkml:prefix_reference ], - [ linkml:prefix_prefix "ECTO" ; - linkml:prefix_reference ], + [ linkml:prefix_prefix "GTEx" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "ORPHA" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "GTOPDB" ; + linkml:prefix_reference ], [ linkml:prefix_prefix "HCPCS" ; linkml:prefix_reference ], - [ linkml:prefix_prefix "issn" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "RTXKG1" ; - linkml:prefix_reference ], + [ linkml:prefix_prefix "ExO" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "WBVocab" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "STY" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "hetio" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "linkml" ; + linkml:prefix_reference linkml: ], + [ linkml:prefix_prefix "MI" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "CLINVAR" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "WIKIDATA_PROPERTY" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "EFO" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "HsapDv" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "RXCUI" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "foodb.compound" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "KEGG.BRITE" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "DGIdb" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "PHAROS" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "gpi" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "WIKIDATA" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "KEGG.PATHWAY" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "KEGG.RCLASS" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "OBAN" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "qud" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "GOP" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "mirbase" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "SNPEFF" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "CHEMBL.MECHANISM" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "isbn" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "DrugCentral" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "biolink" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "EDAM-DATA" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "ECTO" ; + linkml:prefix_reference ], [ linkml:prefix_prefix "dcat" ; linkml:prefix_reference ], - [ linkml:prefix_prefix "GSID" ; - linkml:prefix_reference ], + [ linkml:prefix_prefix "NDDF" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "SEMMEDDB" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "doi" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "MAXO" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "alliancegenome" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "ResearchID" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "NLMID" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "ScopusID" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "SNOMED" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "Xenbase" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "pav" ; + linkml:prefix_reference pav: ], + [ linkml:prefix_prefix "oboformat" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "EDAM-OPERATION" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "SIO" ; + linkml:prefix_reference ], [ linkml:prefix_prefix "PATO-PROPERTY" ; linkml:prefix_reference ], - [ linkml:prefix_prefix "PathWhiz" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "LOINC" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "INO" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "foaf" ; - linkml:prefix_reference ], + [ linkml:prefix_prefix "GOREL" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "CAID" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "SNOMEDCT" ; + linkml:prefix_reference ], [ linkml:prefix_prefix "EDAM-TOPIC" ; linkml:prefix_reference ], - [ linkml:prefix_prefix "KEGG.DGROUP" ; - linkml:prefix_reference ], + [ linkml:prefix_prefix "foaf" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "issn" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "REPODB" ; + linkml:prefix_reference ], [ linkml:prefix_prefix "ORCID" ; linkml:prefix_reference ], - [ linkml:prefix_prefix "CAID" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "ChemBank" ; - linkml:prefix_reference ], [ linkml:prefix_prefix "PDQ" ; linkml:prefix_reference ], - [ linkml:prefix_prefix "CPT" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "ORPHA" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "Xenbase" ; - linkml:prefix_reference ], [ linkml:prefix_prefix "XPO" ; linkml:prefix_reference ], - [ linkml:prefix_prefix "METANETX.REACTION" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "DGIdb" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "MSigDB" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "EDAM-FORMAT" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "ScopusID" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "EDAM-OPERATION" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "CHEMBL.MECHANISM" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "CTD" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "WIKIDATA" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "NLMID" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "os" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "HsapDv" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "mirbase" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "SNOMEDCT" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "gpi" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "GOP" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "RO" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "KEGG.ENZYME" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "SNOMED" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "alliancegenome" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "oboformat" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "ResearchID" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "RXNORM" ; - linkml:prefix_reference ], + [ linkml:prefix_prefix "NCBIGene" ; + linkml:prefix_reference ], [ linkml:prefix_prefix "MetaCyc" ; linkml:prefix_reference ], [ linkml:prefix_prefix "PANTHER.FAMILY" ; linkml:prefix_reference ], - [ linkml:prefix_prefix "ICD10" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "chembio" ; - linkml:prefix_reference ], + [ linkml:prefix_prefix "interpro" ; + linkml:prefix_reference ], [ linkml:prefix_prefix "OBOREL" ; linkml:prefix_reference ], - [ linkml:prefix_prefix "KEGG.GENE" ; - linkml:prefix_reference ], + [ linkml:prefix_prefix "fabio" ; + linkml:prefix_reference ], [ linkml:prefix_prefix "SEED.REACTION" ; linkml:prefix_reference ], - [ linkml:prefix_prefix "isbn" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "MI" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "GAMMA" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "CLINVAR" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "GTEx" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "prov" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "EFO" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "MAXO" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "VANDF" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "gff3" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "Aeolus" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "HANCESTRO" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "doi" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "biolink" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "hetio" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "schema" ; - linkml:prefix_reference schema: ], + [ linkml:prefix_prefix "METANETX.REACTION" ; + linkml:prefix_reference ], [ linkml:prefix_prefix "UMLSSG" ; linkml:prefix_reference ], - [ linkml:prefix_prefix "ExO" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "dct" ; - linkml:prefix_reference dcterms: ], - [ linkml:prefix_prefix "gtpo" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "pav" ; - linkml:prefix_reference pav: ], - [ linkml:prefix_prefix "FYPO" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "DrugCentral" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "CID" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "ICD0" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "interpro" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "fabio" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "OBAN" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "SIO" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "qud" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "wgs" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "EDAM-DATA" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "SEMMEDDB" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "GTOPDB" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "linkml" ; - linkml:prefix_reference linkml: ], - [ linkml:prefix_prefix "SNPEFF" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "WIKIDATA_PROPERTY" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "NCBIGene" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "NDDF" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "KEGG.RCLASS" ; + [ linkml:prefix_prefix "KEGG.GENE" ; linkml:prefix_reference ], - [ linkml:prefix_prefix "MESH" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "COG" ; - linkml:prefix_reference ] ; + [ linkml:prefix_prefix "CPT" ; + linkml:prefix_reference ] ; linkml:slots , , , @@ -1139,7 +1139,7 @@ , ; linkml:source_file "biolink-model.yaml" ; - linkml:source_file_date "Mon Oct 25 15:40:24 2021"^^xsd:dateTime ; + linkml:source_file_date "Mon Oct 25 15:58:19 2021"^^xsd:dateTime ; linkml:source_file_size 323656 ; linkml:subsets , , @@ -2267,11 +2267,11 @@ linkml:domain ; linkml:domain_of ; linkml:examples [ a linkml:Example ; - skos:definition "abnormal brain ventricle size" ; - skos:example "MP:0013229" ], - [ a linkml:Example ; skos:definition "Ehlers-Danlos syndrome, vascular type" ; - skos:example "MONDO:0017314" ] ; + skos:example "MONDO:0017314" ], + [ a linkml:Example ; + skos:definition "abnormal brain ventricle size" ; + skos:example "MP:0013229" ] ; linkml:is_a ; linkml:is_usage_slot true ; linkml:local_names [ linkml:ga4gh [ skos:altLabel "descriptor" ; @@ -2361,14 +2361,14 @@ linkml:domain ; linkml:domain_of ; linkml:examples [ a linkml:Example ; - skos:definition "abnormal circulating bilirubin level" ; - skos:example "MP:0001569" ], + skos:definition "axon morphology variant" ; + skos:example "WBPhenotype:0000180" ], [ a linkml:Example ; skos:definition "Hyperkinesis" ; skos:example "HP:0002487" ], [ a linkml:Example ; - skos:definition "axon morphology variant" ; - skos:example "WBPhenotype:0000180" ] ; + skos:definition "abnormal circulating bilirubin level" ; + skos:example "MP:0001569" ] ; linkml:is_a ; linkml:is_usage_slot true ; linkml:local_names [ linkml:ga4gh [ skos:altLabel "descriptor" ; @@ -6328,11 +6328,11 @@ linkml:domain ; linkml:domain_of ; linkml:examples [ a linkml:Example ; - skos:definition "NM_007294.3(BRCA1):c.2521C>T (p.Arg841Trp)" ; - skos:example "ClinVarVariant:17681" ], - [ a linkml:Example ; skos:definition "ti282a allele from ZFIN" ; - skos:example "ZFIN:ZDB-ALT-980203-1091" ] ; + 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" ] ; linkml:identifier true ; linkml:is_a ; linkml:is_usage_slot true ; @@ -9679,11 +9679,11 @@ 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 ; @@ -14391,11 +14391,11 @@ linkml:inlined true ; linkml:is_a ; linkml:local_names [ a linkml:LocalName ; - skos:altLabel "activity directly regulates activity of" ; - linkml:local_name_source "ro" ], - [ a linkml:LocalName ; skos:altLabel "regulates" ; - linkml:local_name_source "translator" ] ; + linkml:local_name_source "translator" ], + [ a linkml:LocalName ; + skos:altLabel "activity directly regulates activity of" ; + linkml:local_name_source "ro" ] ; linkml:mixins ; linkml:multivalued true ; linkml:owner ; @@ -15038,10 +15038,10 @@ linkml:is_a ; linkml:local_names [ a linkml:LocalName ; skos:altLabel "population" ; - linkml:local_name_source "ga4gh" ], + linkml:local_name_source "agr" ], [ a linkml:LocalName ; skos:altLabel "population" ; - linkml:local_name_source "agr" ] ; + linkml:local_name_source "ga4gh" ] ; linkml:mixins ; linkml:slot_usage [ ] ; linkml:slots , @@ -18755,11 +18755,11 @@ 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 "A contiguous change at a Location" ; - 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:source "AGR" ], + [ a linkml:AltDescription ; + skos:definition "A contiguous change at a Location" ; + linkml:source "VMC" ] ; linkml:class_uri ; linkml:definition_uri ; linkml:id_prefixes "CAID", @@ -19105,11 +19105,11 @@ 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 "predicate" ; - linkml:local_name_source "translator" ], - [ a linkml:LocalName ; skos:altLabel "annotation predicate" ; - linkml:local_name_source "ga4gh" ] ; + linkml:local_name_source "ga4gh" ], + [ a linkml:LocalName ; + skos:altLabel "predicate" ; + linkml:local_name_source "translator" ] ; linkml:owner ; linkml:range ; linkml:required true ; @@ -19216,11 +19216,11 @@ 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 "node with incoming relationship" ; - linkml:local_name_source "neo4j" ], - [ a linkml:LocalName ; skos:altLabel "descriptor" ; - linkml:local_name_source "ga4gh" ] ; + linkml:local_name_source "ga4gh" ], + [ a linkml:LocalName ; + skos:altLabel "node with incoming relationship" ; + linkml:local_name_source "neo4j" ] ; linkml:owner ; linkml:range ; linkml:required true ; diff --git a/biolink/model.py b/biolink/model.py index 56b33a3aad..cd76d55b20 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: 2021-10-25 15:43 +# Generation date: 2021-10-25 16:01 # Schema: Biolink-Model # # id: https://w3id.org/biolink/biolink-model diff --git a/context.jsonld b/context.jsonld index 2608827147..0b86a90016 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: 2021-10-25 15:43\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: 2021-10-25 16:00\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_", diff --git a/contextn.jsonld b/contextn.jsonld index e4fffb397a..3c898b3ff8 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: 2021-10-25 15:43\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: 2021-10-25 16:00\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_",