From e911ce3109a7b95c210faa16713a89e1f96c6379 Mon Sep 17 00:00:00 2001 From: GitHub Action Date: Wed, 5 Jan 2022 17:43:34 +0000 Subject: [PATCH] Regenerate artifacts from biolink-model.yaml --- biolink-model.owl.ttl | 724 +++++++++++++++++++++--------------------- biolink-model.ttl | 442 +++++++++++++------------- biolink/model.py | 2 +- context.jsonld | 2 +- contextn.jsonld | 2 +- 5 files changed, 586 insertions(+), 586 deletions(-) diff --git a/biolink-model.owl.ttl b/biolink-model.owl.ttl index f04a522220..e7efc51352 100644 --- a/biolink-model.owl.ttl +++ b/biolink-model.owl.ttl @@ -76,12 +76,12 @@ dcat:downloadURL a owl:ObjectProperty . biolink:ThingWithTaxon, biolink:VariantToEntityAssociationMixin ; dct:license "https://creativecommons.org/publicdomain/zero/1.0/" ; - pav:version "2.2.12" ; + pav:version "2.2.13" ; skos:definition "Entity and association taxonomy and datamodel for life-sciences data" ; - linkml:generation_date "2022-01-05T00:55:16" ; + linkml:generation_date "2022-01-05T17:41:24" ; linkml:metamodel_version "1.7.0" ; linkml:source_file "biolink-model.yaml" ; - linkml:source_file_date "2022-01-05T00:53:16" ; + linkml:source_file_date "2022-01-05T17:39:22" ; linkml:source_file_size 322466 . biolink:Activity a owl:Class ; @@ -103,10 +103,6 @@ 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 ], @@ -114,12 +110,20 @@ biolink:AnatomicalEntityToAnatomicalEntityOntogenicAssociation a owl:Class ; 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 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." . biolink:AnatomicalEntityToAnatomicalEntityPartOfAssociation a owl:Class ; rdfs:label "anatomical entity to anatomical entity part of 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 ], @@ -127,42 +131,38 @@ biolink:AnatomicalEntityToAnatomicalEntityPartOfAssociation a owl:Class ; 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: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:maxQualifiedCardinality 1 ; owl:onClass linkml:String ; - owl:onProperty biolink:issue ], - [ a owl:Restriction ; - owl:onClass linkml:Uriorcurie ; - owl:onProperty biolink:published_in ; - owl:qualifiedCardinality 1 ], + owl:onProperty biolink:volume ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass linkml:String ; - owl:onProperty biolink:volume ], + owl:onProperty biolink:issue ], 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:FrequencyValue ; - owl:onProperty biolink:frequency_qualifier ], + owl:onClass biolink:Onset ; + owl:onProperty biolink:onset_qualifier ], [ a owl:Restriction ; - owl:onClass biolink:BehavioralFeature ; - owl:onProperty rdf:object ; + owl:onClass biolink:Behavior ; + owl:onProperty rdf:subject ; owl:qualifiedCardinality 1 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; @@ -170,16 +170,16 @@ biolink:BehaviorToBehavioralFeatureAssociation a owl:Class ; owl:onProperty biolink:severity_qualifier ], [ 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:onClass biolink:Behavior ; - owl:onProperty rdf:subject ; + owl:onClass biolink:BehavioralFeature ; + owl:onProperty rdf:object ; owl:qualifiedCardinality 1 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:Onset ; - owl:onProperty biolink:onset_qualifier ], + owl:onClass biolink:BiologicalSex ; + owl:onProperty biolink:sex_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." . @@ -213,11 +213,11 @@ 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." . @@ -228,10 +228,6 @@ biolink:CaseToPhenotypicFeatureAssociation a owl:Class ; 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 ; @@ -240,6 +236,10 @@ biolink:CaseToPhenotypicFeatureAssociation a owl:Class ; 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 ], biolink:Association, biolink:CaseToEntityAssociationMixin, biolink:EntityToPhenotypicFeatureAssociationMixin ; @@ -257,10 +257,6 @@ biolink:Cell a owl:Class ; biolink:CellLineAsAModelOfDiseaseAssociation a owl:Class ; rdfs:label "cell line as a model of disease association" ; rdfs:subClassOf [ a owl:Restriction ; - owl: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 ], @@ -268,6 +264,10 @@ biolink:CellLineAsAModelOfDiseaseAssociation a owl:Class ; 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 ; @@ -280,18 +280,18 @@ biolink:ChemicalToChemicalDerivationAssociation a owl:Class ; rdfs:label "chemical to chemical derivation association" ; rdfs:subClassOf [ a owl:Restriction ; owl:onClass biolink:ChemicalEntity ; - owl:onProperty rdf:subject ; + 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:allValuesFrom biolink:MacromolecularMachineMixin ; + owl:onProperty biolink:catalyst_qualifier ], [ a owl:Restriction ; owl:onClass biolink:ChemicalEntity ; - owl:onProperty rdf:object ; + owl:onProperty rdf:subject ; 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: @@ -518,26 +518,26 @@ 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" . biolink:ExposureEventToOutcomeAssociation a owl:Class ; rdfs:label "exposure event to outcome association" ; rdfs:subClassOf [ 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 ], + [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass biolink:PopulationOfIndividualOrganisms ; + owl:onProperty biolink:has_population_context ], biolink:Association, biolink:EntityToOutcomeAssociationMixin, biolink:ExposureEventToEntityAssociationMixin ; @@ -546,25 +546,25 @@ 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:BiologicalSex ; + owl:onProperty biolink:sex_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 ], [ 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:FrequencyValue ; owl:onProperty biolink:frequency_qualifier ], + [ 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." . @@ -610,22 +610,18 @@ 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: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 ], + [ a owl:Restriction ; + owl:onClass biolink:GeneOrGeneProduct ; + owl:onProperty rdf:subject ; + owl:qualifiedCardinality 1 ], biolink:GeneToDiseaseAssociation . biolink:GeneRegulatoryRelationship a owl:Class ; rdfs:label "gene regulatory relationship" ; rdfs:subClassOf [ 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 ], @@ -633,6 +629,10 @@ biolink:GeneRegulatoryRelationship a owl:Class ; owl:onClass biolink:GeneOrGeneProduct ; 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 "A regulatory relationship between two genes" . @@ -640,6 +640,10 @@ 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:maxQualifiedCardinality 1 ; + owl:onClass biolink:LifeStage ; + owl:onProperty biolink:stage_qualifier ], + [ a owl:Restriction ; owl:onClass biolink:GeneOrGeneProduct ; owl:onProperty rdf:subject ; owl:qualifiedCardinality 1 ], @@ -651,10 +655,6 @@ biolink:GeneToExpressionSiteAssociation a owl:Class ; 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 ; @@ -667,12 +667,8 @@ biolink:GeneToGeneCoexpressionAssociation a owl:Class ; rdfs:label "gene to gene coexpression association" ; rdfs:subClassOf [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:DiseaseOrPhenotypicFeature ; - owl:onProperty biolink:phenotypic_state ], - [ a owl:Restriction ; - owl:onClass biolink:PredicateType ; - owl:onProperty rdf:predicate ; - owl:qualifiedCardinality 1 ], + owl:onClass biolink:OntologyClass ; + owl:onProperty biolink:quantifier_qualifier ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass biolink:LifeStage ; @@ -681,10 +677,14 @@ biolink:GeneToGeneCoexpressionAssociation a owl:Class ; owl:maxQualifiedCardinality 1 ; owl:onClass biolink:AnatomicalEntity ; owl:onProperty biolink:expression_site ], + [ a owl:Restriction ; + owl:onClass biolink:PredicateType ; + owl:onProperty rdf:predicate ; + owl:qualifiedCardinality 1 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:OntologyClass ; - owl:onProperty biolink:quantifier_qualifier ], + owl:onClass biolink:DiseaseOrPhenotypicFeature ; + owl:onProperty biolink:phenotypic_state ], biolink:GeneExpressionMixin, biolink:GeneToGeneAssociation ; skos:definition "Indicates that two genes are co-expressed, generally under the same conditions." . @@ -701,10 +701,6 @@ 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:Gene ; owl:onProperty rdf:subject ; owl:qualifiedCardinality 1 ], @@ -712,19 +708,23 @@ biolink:GeneToGeneProductRelationship a owl:Class ; 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 ], 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:GeneOntologyClass ; - owl:onProperty rdf:object ; - owl:qualifiedCardinality 1 ], - [ 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 ], biolink:FunctionalAssociation ; skos:altLabel "functional association" ; skos:exactMatch WBVocab:Gene-GO-Association . @@ -732,25 +732,25 @@ 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 ], [ 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: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 ], biolink:Association, biolink:EntityToPhenotypicFeatureAssociationMixin, biolink:GeneToEntityAssociationMixin ; @@ -778,19 +778,19 @@ 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:TimeType ; owl:onProperty biolink:timepoint ], - [ a owl:Restriction ; - 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_or_gene_product ], [ a owl:Restriction ; - owl:allValuesFrom biolink:OrganismTaxon ; - owl:onProperty biolink:in_taxon ], + owl:maxQualifiedCardinality 1 ; + owl:onClass biolink:BiologicalSequence ; + owl:onProperty biolink:has_biological_sequence ], biolink:ExposureEvent, biolink:GeneGroupingMixin, biolink:GenomicEntity, @@ -814,30 +814,30 @@ biolink:GenotypeToGeneAssociation a owl:Class ; owl:onClass biolink:Genotype ; owl:onProperty rdf:subject ; owl:qualifiedCardinality 1 ], - [ 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 ; 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" . biolink:GenotypeToGenotypePartAssociation a owl:Class ; rdfs:label "genotype to genotype part association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:onClass biolink:PredicateType ; - owl:onProperty rdf:predicate ; + 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 ], [ a owl:Restriction ; - owl:onClass biolink:Genotype ; - owl:onProperty rdf:object ; + owl:onClass biolink:PredicateType ; + owl:onProperty rdf:predicate ; owl:qualifiedCardinality 1 ], biolink:Association ; skos:definition "Any association between one genotype and a genotypic entity that is a sub-component of it" . @@ -845,25 +845,25 @@ biolink:GenotypeToGenotypePartAssociation a owl:Class ; biolink:GenotypeToPhenotypicFeatureAssociation a owl:Class ; rdfs:label "genotype to phenotypic feature 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 ], + [ 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 ], [ 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 ], + owl:maxQualifiedCardinality 1 ; + owl:onClass biolink:Onset ; + owl:onProperty biolink:onset_qualifier ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass biolink:FrequencyValue ; @@ -876,10 +876,6 @@ 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 ], @@ -887,6 +883,10 @@ 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." . @@ -974,11 +974,11 @@ 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)." . @@ -1040,14 +1040,14 @@ biolink:MaterialSampleDerivationAssociation a owl:Class ; owl:onClass biolink:PredicateType ; owl:onProperty rdf:predicate ; owl:qualifiedCardinality 1 ], - [ a owl:Restriction ; - owl:onClass biolink:MaterialSample ; - 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:MaterialSample ; + owl:onProperty rdf:subject ; + owl:qualifiedCardinality 1 ], biolink:Association ; skos:definition "An association between a material sample and the material entity from which it is derived." . @@ -1068,13 +1068,13 @@ 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" . @@ -1082,11 +1082,11 @@ 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" . @@ -1105,6 +1105,10 @@ 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:NamedThing ; + owl:onProperty rdf:object ; + owl:qualifiedCardinality 1 ], + [ a owl:Restriction ; owl:onClass biolink:OrganismTaxon ; owl:onProperty rdf:subject ; owl:qualifiedCardinality 1 ], @@ -1112,10 +1116,6 @@ biolink:OrganismTaxonToEnvironmentAssociation a owl:Class ; 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 ], biolink:Association, biolink:OrganismTaxonToEntityAssociation . @@ -1129,14 +1129,14 @@ biolink:OrganismTaxonToOrganismTaxonInteraction a owl:Class ; 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: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" . @@ -1144,11 +1144,11 @@ 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:onProperty rdf:object ; owl:qualifiedCardinality 1 ], [ a owl:Restriction ; owl:onClass biolink:OrganismTaxon ; - owl:onProperty rdf:object ; + owl:onProperty rdf:subject ; owl:qualifiedCardinality 1 ], [ a owl:Restriction ; owl:onClass biolink:PredicateType ; @@ -1161,17 +1161,21 @@ 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:onProperty rdf:subject ; owl:qualifiedCardinality 1 ], [ a owl:Restriction ; owl:onClass biolink:IndividualOrganism ; - owl:onProperty rdf:subject ; + 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:onClass biolink:OrganismalEntity ; + owl:onProperty rdf:subject ; + owl:qualifiedCardinality 1 ], + [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass biolink:Onset ; owl:onProperty biolink:onset_qualifier ], @@ -1183,10 +1187,6 @@ biolink:OrganismalEntityAsAModelOfDiseaseAssociation a owl:Class ; owl:maxQualifiedCardinality 1 ; owl:onClass biolink:SeverityValue ; owl:onProperty biolink:severity_qualifier ], - [ a owl:Restriction ; - owl:onClass biolink:OrganismalEntity ; - owl:onProperty rdf:subject ; - owl:qualifiedCardinality 1 ], biolink:Association, biolink:EntityToDiseaseAssociationMixin, biolink:ModelToDiseaseAssociationMixin . @@ -1194,25 +1194,25 @@ biolink:OrganismalEntityAsAModelOfDiseaseAssociation a owl:Class ; biolink:PairwiseMolecularInteraction a owl:Class ; rdfs:label "pairwise molecular interaction" ; rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:OntologyClass ; - owl:onProperty biolink:interacting_molecules_category ], + owl:onClass linkml:String ; + owl:onProperty biolink:id ; + owl:qualifiedCardinality 1 ], [ a owl:Restriction ; - owl:onClass biolink:MolecularEntity ; - owl:onProperty rdf:object ; + owl:onClass biolink:PredicateType ; + owl:onProperty rdf:predicate ; owl:qualifiedCardinality 1 ], [ a owl:Restriction ; owl:onClass biolink:MolecularEntity ; owl:onProperty rdf:subject ; owl:qualifiedCardinality 1 ], [ a owl:Restriction ; - owl:onClass biolink:PredicateType ; - owl:onProperty rdf:predicate ; + 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 ], + owl:maxQualifiedCardinality 1 ; + owl:onClass biolink:OntologyClass ; + owl:onProperty biolink:interacting_molecules_category ], biolink:PairwiseGeneToGeneInteraction ; skos:definition "An interaction at the molecular level between two physical entities" . @@ -1416,13 +1416,13 @@ 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:SequenceVariant ; - owl:onProperty rdf:subject ; - owl:qualifiedCardinality 1 ], - [ 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 ], 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" . @@ -1433,14 +1433,14 @@ biolink:Serial a owl:Class ; owl:onClass linkml:String ; owl:onProperty biolink:id ; owl:qualifiedCardinality 1 ], - [ 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 ], + [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass linkml:String ; + owl:onProperty biolink:iso_abbreviation ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass linkml:String ; @@ -1448,7 +1448,7 @@ biolink:Serial a owl:Class ; [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass linkml:String ; - owl:onProperty biolink:iso_abbreviation ], + owl:onProperty biolink:volume ], biolink:Publication ; skos:altLabel "journal" ; skos:definition "This class may rarely be instantiated except if use cases of a given knowledge graph support its utility." . @@ -1508,11 +1508,11 @@ 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:onClass biolink:OrganismTaxon ; - owl:onProperty rdf:subject ; + owl:onProperty rdf:object ; owl:qualifiedCardinality 1 ], biolink:Association . @@ -1551,22 +1551,22 @@ biolink:VariantToGeneExpressionAssociation a owl:Class ; 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:AnatomicalEntity ; owl:onProperty biolink:expression_site ], [ 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:onClass biolink:PredicateType ; owl:onProperty rdf:predicate ; owl:qualifiedCardinality 1 ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:OntologyClass ; - owl:onProperty biolink:quantifier_qualifier ], biolink:GeneExpressionMixin, biolink:VariantToGeneAssociation ; skos:definition "An association between a variant and expression of a gene (i.e. e-QTL)" . @@ -1574,13 +1574,13 @@ biolink:VariantToGeneExpressionAssociation a owl:Class ; biolink:VariantToPhenotypicFeatureAssociation a owl:Class ; rdfs:label "variant to phenotypic feature association" ; rdfs:subClassOf [ 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 ], + [ 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 ; @@ -1600,9 +1600,17 @@ biolink:VariantToPhenotypicFeatureAssociation a owl:Class ; biolink:VariantToPopulationAssociation a owl:Class ; rdfs:label "variant to population association" ; rdfs:subClassOf [ 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 ], + [ a owl:Restriction ; + owl:onClass biolink:SequenceVariant ; + owl:onProperty rdf:subject ; + owl:qualifiedCardinality 1 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass linkml:Double ; @@ -1611,22 +1619,14 @@ biolink:VariantToPopulationAssociation a owl:Class ; owl:onClass biolink:PopulationOfIndividualOrganisms ; 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:maxQualifiedCardinality 1 ; - owl:onClass biolink:FrequencyValue ; - owl:onProperty biolink:frequency_qualifier ], [ 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 ], + owl:onClass biolink:FrequencyValue ; + owl:onProperty biolink:frequency_qualifier ], biolink:Association, biolink:FrequencyQualifierMixin, biolink:FrequencyQuantifier, @@ -2150,6 +2150,10 @@ biolink:BehavioralFeature a owl:Class ; biolink:BookChapter a owl:Class ; rdfs:label "book chapter" ; rdfs:subClassOf [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass linkml:String ; + owl:onProperty biolink:chapter ], + [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass linkml:String ; owl:onProperty biolink:volume ], @@ -2157,10 +2161,6 @@ biolink:BookChapter a owl:Class ; 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:chapter ], biolink:Publication . biolink:Case a owl:Class ; @@ -2279,13 +2279,13 @@ 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:Integer ; - owl:onProperty biolink:has_count ], - [ 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_count ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass linkml:Integer ; @@ -2303,14 +2303,14 @@ biolink:GenotypeToDiseaseAssociation 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: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 ], [ a owl:Restriction ; owl:onClass biolink:PredicateType ; owl:onProperty rdf:predicate ; @@ -2321,8 +2321,8 @@ biolink:GenotypeToDiseaseAssociation a owl:Class ; owl:qualifiedCardinality 1 ], [ 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 ; @@ -2333,11 +2333,11 @@ biolink:GeographicLocation a owl:Class ; rdfs:subClassOf [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass linkml:Float ; - owl:onProperty biolink:longitude ], + owl:onProperty biolink:latitude ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass linkml:Float ; - owl:onProperty biolink:latitude ], + owl:onProperty biolink:longitude ], biolink:PlanetaryEntity ; skos:definition "a location that can be described in lat/long coordinates" ; skos:exactMatch STY:T083, @@ -2390,9 +2390,9 @@ biolink:Polypeptide a owl:Class ; biolink:ReactionToParticipantAssociation a owl:Class ; rdfs:label "reaction to participant association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:onClass biolink:MolecularEntity ; - owl:onProperty rdf:subject ; - owl:qualifiedCardinality 1 ], + owl:maxQualifiedCardinality 1 ; + owl:onClass linkml:Integer ; + owl:onProperty biolink:stoichiometry ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass ; @@ -2402,9 +2402,9 @@ biolink:ReactionToParticipantAssociation a owl:Class ; owl:onClass ; owl:onProperty biolink:reaction_direction ], [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:Integer ; - owl:onProperty biolink:stoichiometry ], + owl:onClass biolink:MolecularEntity ; + owl:onProperty rdf:subject ; + owl:qualifiedCardinality 1 ], biolink:ChemicalToChemicalAssociation . biolink:SequenceAssociation a owl:Class ; @@ -2436,18 +2436,18 @@ biolink:TaxonomicRank a owl:Class ; biolink:Treatment a owl:Class ; rdfs:label "treatment" ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom biolink:Procedure ; - owl:onProperty biolink:has_procedure ], - [ 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 ], [ a owl:Restriction ; owl:allValuesFrom biolink:Device ; owl:onProperty biolink:has_device ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:Procedure ; + owl:onProperty biolink:has_procedure ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:Drug ; + owl:onProperty biolink:has_drug ], biolink:ChemicalOrDrugOrTreatment, biolink:ExposureEvent, biolink:NamedThing ; @@ -2461,20 +2461,12 @@ 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: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: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 ], [ a owl:Restriction ; owl:onClass biolink:PredicateType ; @@ -2484,6 +2476,14 @@ biolink:VariantToDiseaseAssociation a owl:Class ; 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 ], biolink:Association, biolink:EntityToDiseaseAssociationMixin, biolink:VariantToEntityAssociationMixin ; @@ -2492,13 +2492,13 @@ 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)" . @@ -4343,11 +4343,11 @@ 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 . @@ -4483,10 +4483,6 @@ biolink:GeneProductIsoformMixin a owl:Class ; 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 ], - [ a owl:Restriction ; owl:onClass biolink:GeneOrGeneProduct ; owl:onProperty rdf:subject ; owl:qualifiedCardinality 1 ], @@ -4498,6 +4494,10 @@ biolink:GeneToDiseaseAssociation 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 ], biolink:Association, biolink:EntityToDiseaseAssociationMixin, biolink:GeneToEntityAssociationMixin ; @@ -4552,11 +4552,11 @@ biolink:OrganismTaxonToOrganismTaxonAssociation a owl:Class ; rdfs:label "organism taxon to organism taxon association" ; rdfs:subClassOf [ a owl:Restriction ; owl:onClass biolink:OrganismTaxon ; - owl:onProperty rdf:subject ; + 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:Association, biolink:OrganismTaxonToEntityAssociation ; @@ -4577,11 +4577,11 @@ 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 , @@ -4828,11 +4828,11 @@ 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." . @@ -4847,38 +4847,38 @@ biolink:DiseaseToEntityAssociationMixin a owl:Class ; biolink:Entity a owl:Class ; rdfs:label "entity" ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom biolink:Attribute ; - owl:onProperty biolink:has_attribute ], - [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass biolink:LabelType ; owl:onProperty biolink:source ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:NarrativeText ; - owl:onProperty dct:description ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:IriType ; - owl:onProperty biolink:iri ], + owl:onClass biolink:LabelType ; + owl:onProperty rdfs:label ], [ a owl:Restriction ; - owl:allValuesFrom biolink:Agent ; - owl:onProperty biolink:provided_by ], + owl:allValuesFrom biolink:CategoryType ; + owl:onProperty biolink:category ], [ a owl:Restriction ; 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 rdf:type ], [ a owl:Restriction ; - owl:allValuesFrom biolink:CategoryType ; - owl:onProperty biolink:category ] ; + owl:maxQualifiedCardinality 1 ; + owl:onClass biolink:IriType ; + owl:onProperty biolink:iri ], + [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass biolink:NarrativeText ; + owl:onProperty dct:description ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:Agent ; + owl:onProperty biolink:provided_by ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:Attribute ; + owl:onProperty biolink:has_attribute ] ; skos:definition "Root Biolink Model class for all things and informational relationships, real or imagined." . biolink:FrequencyQualifierMixin a owl:Class ; @@ -4893,10 +4893,6 @@ biolink:FrequencyQualifierMixin a owl:Class ; biolink:GeneExpressionMixin a owl:Class ; rdfs:label "gene expression mixin" ; rdfs:subClassOf [ 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 ], @@ -4908,6 +4904,10 @@ 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 ], linkml:mixin ; skos:definition "Observed gene expression intensity, context (site, stage) and associated phenotypic status within which the expression occurs." . @@ -5395,13 +5395,13 @@ biolink:ClinicalAttribute a owl:Class ; biolink:DatasetVersion a owl:Class ; rdfs:label "dataset version" ; rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass 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:Dataset ; + owl:onProperty dct:source ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass biolink:DatasetDistribution ; @@ -5665,11 +5665,11 @@ biolink:GeneGroupingMixin 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." ; @@ -5689,13 +5689,13 @@ biolink:MacromolecularMachineMixin a owl:Class ; biolink:ModelToDiseaseAssociationMixin a owl:Class ; rdfs:label "model to disease association mixin" ; 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:onClass biolink:PredicateType ; + owl:onProperty rdf:predicate ; + owl:qualifiedCardinality 1 ], linkml:mixin ; skos:definition "This mixin is used for any association class for which the subject (source node) plays the role of a 'model', in that it recapitulates some features of the disease in a way that is useful for studying the disease outside a patient carrying the disease" . @@ -5766,16 +5766,16 @@ biolink:EntityToPhenotypicFeatureAssociationMixin a owl:Class ; biolink:Genotype a owl:Class ; rdfs:label "genotype" ; rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:Zygosity ; - owl:onProperty biolink:has_zygosity ], + 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 ], + owl:maxQualifiedCardinality 1 ; + owl:onClass biolink:Zygosity ; + owl:onProperty biolink:has_zygosity ], biolink:BiologicalEntity, biolink:GenomicEntity, biolink:OntologyClass, @@ -5827,14 +5827,14 @@ biolink:GenomicEntity a owl:Class ; biolink:MolecularActivity a owl:Class ; rdfs:label "molecular activity" ; rdfs:subClassOf [ 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_output ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:MolecularEntity ; + owl:onProperty biolink:has_input ], biolink:BiologicalProcessOrActivity, biolink:Occurrent, biolink:OntologyClass ; @@ -5872,20 +5872,20 @@ 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 ], - [ a owl:Restriction ; owl:allValuesFrom linkml:Uriorcurie ; owl:onProperty biolink:affiliation ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty biolink:address ], + owl:onClass biolink:LabelType ; + owl:onProperty rdfs:label ], [ a owl:Restriction ; owl:onClass linkml:String ; owl:onProperty biolink:id ; owl:qualifiedCardinality 1 ], + [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass linkml:String ; + owl:onProperty biolink:address ], biolink:AdministrativeEntity ; skos:altLabel "group" ; skos:definition "person, group, organization or project that provides a piece of information (i.e. a knowledge association)" ; @@ -5922,36 +5922,36 @@ biolink:GenomicSequenceLocalization a owl:Class ; rdfs:label "genomic sequence localization" ; rdfs:subClassOf [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass ; - owl:onProperty biolink:genome_build ], + owl:onClass linkml:Integer ; + owl:onProperty biolink:start_interbase_coordinate ], [ a owl:Restriction ; - owl:onClass biolink:NucleicAcidEntity ; - owl:onProperty rdf:object ; - owl:qualifiedCardinality 1 ], + owl:maxQualifiedCardinality 1 ; + owl:onClass ; + owl:onProperty biolink:phase ], [ a owl:Restriction ; owl:onClass biolink:PredicateType ; owl:onProperty rdf:predicate ; owl:qualifiedCardinality 1 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass ; - owl:onProperty biolink:phase ], + owl:onClass ; + owl:onProperty biolink:strand ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:Integer ; - owl:onProperty biolink:start_interbase_coordinate ], + owl:onClass ; + owl:onProperty biolink:genome_build ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass linkml:Integer ; owl:onProperty biolink:end_interbase_coordinate ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass ; - owl:onProperty biolink:strand ], [ a owl:Restriction ; 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 ], biolink:SequenceAssociation ; skos:broadMatch dcid:Chromosome ; skos:definition "A relationship between a sequence feature and a nucleic acid entity it is localized to. The reference entity may be a chromosome, chromosome region or information entity such as a contig." ; @@ -5965,25 +5965,25 @@ biolink:Attribute a owl:Class ; owl:onClass biolink:OntologyClass ; owl:onProperty biolink:has_attribute_type ; owl:qualifiedCardinality 1 ], + [ 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 rdfs:label ], [ 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:LabelType ; owl:onProperty biolink:source ], + [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass biolink:LabelType ; + owl:onProperty rdfs:label ], 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." ; @@ -6071,14 +6071,14 @@ biolink:InformationContentEntity a owl:Class ; owl:maxQualifiedCardinality 1 ; owl:onClass linkml:String ; owl:onProperty biolink:license ], - [ 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", @@ -6136,33 +6136,33 @@ biolink:Publication a owl:Class ; owl:maxQualifiedCardinality 1 ; owl:onClass biolink:LabelType ; owl:onProperty rdfs:label ], - [ a owl:Restriction ; - owl:onClass linkml:String ; - owl:onProperty biolink:id ; - owl:qualifiedCardinality 1 ], [ a owl:Restriction ; owl:allValuesFrom linkml:String ; - owl:onProperty biolink:pages ], + owl:onProperty biolink:authors ], + [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass linkml:String ; + owl:onProperty biolink:summary ], [ 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:allValuesFrom linkml:String ; - owl:onProperty biolink:authors ], + owl:onProperty biolink:pages ], [ a owl:Restriction ; owl:allValuesFrom linkml:Uriorcurie ; owl:onProperty biolink:mesh_terms ], [ a owl:Restriction ; owl:onClass linkml:String ; - owl:onProperty dct:type ; + owl:onProperty biolink:id ; owl:qualifiedCardinality 1 ], [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; owl:onClass linkml:String ; - owl:onProperty biolink:summary ], + owl:onProperty dct:type ; + owl:qualifiedCardinality 1 ], + [ a owl:Restriction ; + owl:allValuesFrom linkml:String ; + owl:onProperty biolink:keywords ], biolink:InformationContentEntity ; skos:definition "Any published piece of information. Can refer to a whole publication, its encompassing publication (i.e. journal or book) or to a part of a publication, if of significant knowledge scope (e.g. a figure, figure legend, or section highlighted by NLP). The scope is intended to be general and include information published on the web, as well as printed materials, either directly or in one of the Publication Biolink category subclasses." ; skos:exactMatch IAO:0000311 ; @@ -6262,6 +6262,9 @@ 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 ; @@ -6269,9 +6272,6 @@ 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, @@ -6336,13 +6336,13 @@ biolink:PredicateType 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 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 ; @@ -6391,22 +6391,22 @@ biolink:association_slot a owl:ObjectProperty ; biolink:Gene a owl:Class ; rdfs:label "gene" ; rdfs:subClassOf [ 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 ], + owl:allValuesFrom biolink:LabelType ; + owl:onProperty biolink:synonym ], [ 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 ], [ a owl:Restriction ; owl:allValuesFrom linkml:Uriorcurie ; owl:onProperty biolink:xref ], [ a owl:Restriction ; - owl:allValuesFrom biolink:LabelType ; - owl:onProperty biolink:synonym ], + owl:maxQualifiedCardinality 1 ; + owl:onClass linkml:String ; + owl:onProperty biolink:symbol ], biolink:BiologicalEntity, biolink:ChemicalEntityOrGeneOrGeneProduct, biolink:GeneOrGeneProduct, @@ -6466,8 +6466,23 @@ biolink:related_to_at_instance_level a owl:ObjectProperty, biolink:Association a owl:Class ; rdfs:label "association" ; rdfs:subClassOf [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass linkml:Boolean ; + owl:onProperty biolink:negated ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:OntologyClass ; + owl:onProperty biolink:qualifiers ], + [ a owl:Restriction ; + owl:onClass biolink:NamedThing ; + owl:onProperty rdf:subject ; + owl:qualifiedCardinality 1 ], + [ a owl:Restriction ; owl:allValuesFrom biolink:EvidenceType ; owl:onProperty biolink:has_evidence ], + [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass linkml:String ; + owl:onProperty rdf:type ], [ a owl:Restriction ; owl:onClass biolink:NamedThing ; owl:onProperty rdf:object ; @@ -6476,31 +6491,16 @@ biolink:Association a owl:Class ; owl:allValuesFrom biolink:Publication ; owl:onProperty biolink:publications ], [ a owl:Restriction ; - owl:onClass biolink:NamedThing ; - owl:onProperty rdf:subject ; + owl:onClass biolink:PredicateType ; + owl:onProperty rdf:predicate ; owl:qualifiedCardinality 1 ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:OntologyClass ; - owl:onProperty biolink:qualifiers ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty biolink:relation ], [ 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 ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:Boolean ; - owl:onProperty biolink:negated ], - [ a owl:Restriction ; - owl:onClass biolink:PredicateType ; - owl:onProperty rdf:predicate ; - owl:qualifiedCardinality 1 ], + owl:onProperty biolink:relation ], 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 49fb478f6e..27d85edf62 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 "2.2.12" ; + pav:version "2.2.13" ; skos:definition "Entity and association taxonomy and datamodel for life-sciences data" ; linkml:classes , , @@ -299,236 +299,236 @@ , , ; - linkml:generation_date "2022-01-05T00:55:34"^^xsd:dateTime ; + linkml:generation_date "2022-01-05T17:41:42"^^xsd:dateTime ; linkml:id ; linkml:imports linkml:types ; linkml:metamodel_version "1.7.0" ; - linkml:prefixes [ linkml:prefix_prefix "GOREL" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "qud" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "KEGG.GENE" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "NLMID" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "RO" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "doi" ; + linkml:prefixes [ linkml:prefix_prefix "doi" ; linkml:prefix_reference ], - [ linkml:prefix_prefix "GTEx" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "OBAN" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "MAXO" ; - linkml:prefix_reference ], + [ linkml:prefix_prefix "CTD" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "CID" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "wgs" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "CPT" ; + linkml:prefix_reference ], [ linkml:prefix_prefix "PHAROS" ; linkml:prefix_reference ], - [ linkml:prefix_prefix "fabio" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "VMC" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "EDAM-FORMAT" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "LOINC" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "RXCUI" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "CTD.DISEASE" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "MESH" ; - linkml:prefix_reference ], + [ linkml:prefix_prefix "CAID" ; + linkml:prefix_reference ], [ linkml:prefix_prefix "ORPHA" ; linkml:prefix_reference ], - [ linkml:prefix_prefix "DGIdb" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "pav" ; - linkml:prefix_reference pav: ], - [ linkml:prefix_prefix "foaf" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "UO-PROPERTY" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "UBERON_NONAMESPACE" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "CHADO" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "UBERON_CORE" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "CHEMBL.MECHANISM" ; - linkml:prefix_reference ], [ linkml:prefix_prefix "MI" ; linkml:prefix_reference ], - [ linkml:prefix_prefix "os" ; - linkml:prefix_reference ], + [ linkml:prefix_prefix "ECTO" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "linkml" ; + linkml:prefix_reference linkml: ], + [ linkml:prefix_prefix "gpi" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "PathWhiz" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "KEGG.ENZYME" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "COG" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "SEMMEDDB" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "CHADO" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "isbn" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "KEGG.RCLASS" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "RXNORM" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "dcat" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "OBOREL" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "foaf" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "PANTHER.FAMILY" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "KEGG.BRITE" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "SEED.REACTION" ; + linkml:prefix_reference ], [ linkml:prefix_prefix "EFO" ; linkml:prefix_reference ], - [ linkml:prefix_prefix "METANETX.REACTION" ; - linkml:prefix_reference ], + [ linkml:prefix_prefix "GAMMA" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "WBVocab" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "CHEMBL.MECHANISM" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "GTEx" ; + linkml:prefix_reference ], [ linkml:prefix_prefix "UMLSSG" ; linkml:prefix_reference ], - [ linkml:prefix_prefix "EDAM-DATA" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "gtpo" ; - linkml:prefix_reference ], + [ linkml:prefix_prefix "alliancegenome" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "Xenbase" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "VANDF" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "GOP" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "biolink" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "gff3" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "CLINVAR" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "apollo" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "bioschemas" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "CTD.CHEMICAL" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "mirbase" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "CTD.DISEASE" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "INO" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "VMC" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "metacyc.reaction" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "COAR_RESOURCE" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "RXCUI" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "ICD9" ; + linkml:prefix_reference ], [ linkml:prefix_prefix "dcid" ; linkml:prefix_reference ], [ linkml:prefix_prefix "STY" ; linkml:prefix_reference ], - [ linkml:prefix_prefix "ICD10" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "mirbase" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "foodb.compound" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "CID" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "biolink" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "CAID" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "XPO" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "KEGG.ENZYME" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "issn" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "isbn" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "isni" ; - linkml:prefix_reference ], + [ linkml:prefix_prefix "NCIT-OBO" ; + linkml:prefix_reference ], [ linkml:prefix_prefix "EDAM-TOPIC" ; linkml:prefix_reference ], - [ linkml:prefix_prefix "gpi" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "ExO" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "HANCESTRO" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "CTD.GENE" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "DrugCentral" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "Xenbase" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "GSID" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "CPT" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "SNOMED" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "bioschemas" ; - linkml:prefix_reference ], + [ linkml:prefix_prefix "NLMID" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "WIKIDATA_PROPERTY" ; + linkml:prefix_reference ], [ linkml:prefix_prefix "DOID-PROPERTY" ; linkml:prefix_reference ], - [ linkml:prefix_prefix "KEGG.RCLASS" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "schema" ; - linkml:prefix_reference schema: ], - [ linkml:prefix_prefix "ICD9" ; - linkml:prefix_reference ], + [ linkml:prefix_prefix "HCPCS" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "GSID" ; + linkml:prefix_reference ], [ linkml:prefix_prefix "EDAM-OPERATION" ; linkml:prefix_reference ], - [ linkml:prefix_prefix "SEMMEDDB" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "ORCID" ; - linkml:prefix_reference ], + [ linkml:prefix_prefix "dct" ; + linkml:prefix_reference dcterms: ], + [ linkml:prefix_prefix "XPO" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "KEGG.GENE" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "UBERON_NONAMESPACE" ; + linkml:prefix_reference ], [ linkml:prefix_prefix "medgen" ; linkml:prefix_reference ], - [ linkml:prefix_prefix "HCPCS" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "ECTO" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "metacyc.reaction" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "VANDF" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "PANTHER.FAMILY" ; - linkml:prefix_reference ], + [ linkml:prefix_prefix "DGIdb" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "FYPO" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "KEGG.PATHWAY" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "GTOPDB" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "oboformat" ; + linkml:prefix_reference OIO: ], + [ linkml:prefix_prefix "ORCID" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "ExO" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "EDAM-FORMAT" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "ICD10" ; + linkml:prefix_reference ], [ linkml:prefix_prefix "interpro" ; linkml:prefix_reference ], - [ linkml:prefix_prefix "HsapDv" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "COG" ; - linkml:prefix_reference ], + [ linkml:prefix_prefix "NDDF" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "EDAM-DATA" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "GOREL" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "MESH" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "KEGG.DGROUP" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "UBERON_CORE" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "NCBIGene" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "pav" ; + linkml:prefix_reference pav: ], + [ linkml:prefix_prefix "SIO" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "MAXO" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "fabio" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "LOINC" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "RO" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "DrugCentral" ; + linkml:prefix_reference ], [ linkml:prefix_prefix "WIKIDATA" ; linkml:prefix_reference ], - [ linkml:prefix_prefix "ChemBank" ; - linkml:prefix_reference ], + [ linkml:prefix_prefix "os" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "gtpo" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "HANCESTRO" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "UO-PROPERTY" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "issn" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "ScopusID" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "CTD.GENE" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "UBERGRAPH" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "METANETX.REACTION" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "OBAN" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "SNOMEDCT" ; + linkml:prefix_reference ], [ linkml:prefix_prefix "ResearchID" ; linkml:prefix_reference ], - [ linkml:prefix_prefix "dcat" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "GOP" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "KEGG.BRITE" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "prov" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "NCBIGene" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "gff3" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "KEGG.PATHWAY" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "oboformat" ; - linkml:prefix_reference OIO: ], + [ linkml:prefix_prefix "qud" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "ChemBank" ; + linkml:prefix_reference ], [ linkml:prefix_prefix "MSigDB" ; linkml:prefix_reference ], - [ linkml:prefix_prefix "WIKIDATA_PROPERTY" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "OBOREL" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "WBVocab" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "COAR_RESOURCE" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "PathWhiz" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "CLINVAR" ; - linkml:prefix_reference ], [ linkml:prefix_prefix "REPODB" ; linkml:prefix_reference ], - [ linkml:prefix_prefix "SEED.REACTION" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "alliancegenome" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "KEGG.DGROUP" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "SNOMEDCT" ; + [ linkml:prefix_prefix "isni" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "SNOMED" ; linkml:prefix_reference ], - [ linkml:prefix_prefix "ScopusID" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "wgs" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "GTOPDB" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "dct" ; - linkml:prefix_reference dcterms: ], - [ linkml:prefix_prefix "apollo" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "NCIT-OBO" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "UBERGRAPH" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "GAMMA" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "CTD.CHEMICAL" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "linkml" ; - linkml:prefix_reference linkml: ], - [ linkml:prefix_prefix "RXNORM" ; - linkml:prefix_reference ], [ linkml:prefix_prefix "NBO-PROPERTY" ; linkml:prefix_reference ], - [ linkml:prefix_prefix "CTD" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "INO" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "SIO" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "NDDF" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "FYPO" ; - linkml:prefix_reference ] ; + [ linkml:prefix_prefix "prov" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "HsapDv" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "foodb.compound" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "schema" ; + linkml:prefix_reference schema: ] ; linkml:slots , , , @@ -1153,7 +1153,7 @@ , ; linkml:source_file "biolink-model.yaml" ; - linkml:source_file_date "2022-01-05T00:53:16"^^xsd:dateTime ; + linkml:source_file_date "2022-01-05T17:39:22"^^xsd:dateTime ; linkml:source_file_size 322466 ; linkml:subsets , , @@ -2121,11 +2121,11 @@ 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" ; @@ -9706,11 +9706,11 @@ 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 ; @@ -9750,11 +9750,11 @@ linkml:inlined true ; linkml:is_a ; linkml:local_names [ a linkml:LocalName ; - skos:altLabel "activity directly positively regulates activity of" ; - linkml:local_name_source "ro" ], - [ a linkml:LocalName ; skos:altLabel "positively regulates" ; - linkml:local_name_source "translator" ] ; + linkml:local_name_source "translator" ], + [ a linkml:LocalName ; + skos:altLabel "activity directly positively regulates activity of" ; + linkml:local_name_source "ro" ] ; linkml:mixins ; linkml:multivalued true ; linkml:owner ; @@ -14395,11 +14395,11 @@ linkml:inlined true ; linkml:is_a ; linkml:local_names [ a linkml:LocalName ; - skos:altLabel "regulates" ; - linkml:local_name_source "translator" ], - [ a linkml:LocalName ; skos:altLabel "activity directly regulates activity of" ; - linkml:local_name_source "ro" ] ; + linkml:local_name_source "ro" ], + [ a linkml:LocalName ; + skos:altLabel "regulates" ; + linkml:local_name_source "translator" ] ; linkml:mixins ; linkml:multivalued true ; linkml:owner ; @@ -18774,11 +18774,11 @@ 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", @@ -19180,11 +19180,11 @@ 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 "descriptor" ; - linkml:local_name_source "ga4gh" ], - [ a linkml:LocalName ; skos:altLabel "node with incoming relationship" ; - linkml:local_name_source "neo4j" ] ; + linkml:local_name_source "neo4j" ], + [ a linkml:LocalName ; + skos:altLabel "descriptor" ; + linkml:local_name_source "ga4gh" ] ; linkml:owner ; linkml:range ; linkml:required true ; @@ -19387,11 +19387,11 @@ 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 outgoing relationship" ; - linkml:local_name_source "neo4j" ], - [ a linkml:LocalName ; skos:altLabel "annotation subject" ; - linkml:local_name_source "ga4gh" ] ; + linkml:local_name_source "ga4gh" ], + [ a linkml:LocalName ; + skos:altLabel "node with outgoing relationship" ; + linkml:local_name_source "neo4j" ] ; linkml:owner ; linkml:range ; linkml:required true ; diff --git a/biolink/model.py b/biolink/model.py index d19bd8e5d0..125bc47148 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: 2022-01-05T00:55:47 +# Generation date: 2022-01-05T17:41:54 # Schema: Biolink-Model # # id: https://w3id.org/biolink/biolink-model diff --git a/context.jsonld b/context.jsonld index 659724efe3..5ee70c18f5 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: 2022-01-05T00:55:07\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: 2022-01-05T17:41:15\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 575b5ad0c5..d3ce8a742e 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: 2022-01-05T00:55:12\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: 2022-01-05T17:41:20\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_",